Versatile genetic assembly system (vegas) to assemble pathways for expression

ABSTRACT

Provided are compositions and methods for use in assembling and expressing a plurality of transcription units using, in one aspect, homologous recombination in yeast. Yeast containing the plurality of transcription units, and isolated transcription units, are also provided. Kits for use in making the yeast and the transcript units are further included.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional patent applicationNo. 62/013,321, filed Jun. 17, 2014, the disclosure of which isincorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under contract no.MCB-0718846 awarded by National Science Foundation and under contractno. N66001-12-C-4020 awarded by the Defense Advanced Research ProjectsAgency. The government has certain rights in the invention.

BACKGROUND OF THE DISCLOSURE

S. cerevisiae is a prominent model organism and a highly valued chassisin the field of synthetic biology. In this space, metabolic engineeringis a major focus, as the expression of one or more heterologous enzymescan transform S. cerevisiae into a tiny cellular factory. The mostwell-known example of this to date is the engineering of S. cerevisiaeto produce commercially relevant concentrations of artemisinic acid, aprecursor to the anti-malarial drug artemisinin. These metabolicengineering projects require both the introduction of heterologous geneswhose expression levels are finely tuned, and the redirection ofendogenous biosynthetic pathways via modification of native genes. Thedevelopment of tools to aid in construction and manipulation of bothnative and non-native genes for expression in S. cerevisiae thusfacilitates metabolic engineering and synthetic biology in yeast.

Typical yeast protein coding genes have a relatively simple anatomy, duein part to the compact structure of the S. cerevisiae genome. Promotersare short, generally extending only ˜500 bp upstream of the start codon.Only ˜20% of promoters in the yeast genome contain TATA boxes. Onaverage, native coding sequences (CDS) are ˜1 kb long and less than 5%contain introns. Sequences associated with 3′ end formation, whichtypically extend ˜200 bp downstream of the stop codon, are usuallyAT-rich and contain information for both transcriptional termination and3′ end processing. The simple structure of yeast genes means thatexpression of non-native proteins in yeast can be achieved by encodingthe CDS of interest between a promoter and terminator that can functionin S. cerevisiae. Tuning of CDS expression level can then beaccomplished by varying the promoter and terminator sequences, changingthe gene copy number (e.g. high or low copy plasmid), or altering thegenomic locus in which the gene is integrated.

The production of high-value metabolites in microorganisms suited toindustrial scale growth can overcome costly issues associated withtraditional production routes, including yield, extraction, orcomplicated synthesis procedures. To achieve this, the biosyntheticpathway of interest must be re-constructed in an appropriate hostorganism, typically chosen because it is well characterized andgenetically tractable. Saccharomyces cerevisiae is a favored eukaryoticmicroorganism for metabolic engineering because it is industriallyrobust, generally regarded as safe, and highly amenable to and tolerantof genetic manipulation. Many recent successes in the metabolicengineering of S. cerevisiae have been described, most notably thecost-effective production of artemisinic acid, a precursor to theanti-malarial drug artemisinin. Engineering of the host genome toredirect endogenous pathways and optimizing the expression levels ofnon-native biosynthetic genes are keys to successful metabolicengineering projects. However, there remain significant challenges toefficiently assembling biosynthetic pathways and other gene sets forexpression in S. cerevisiae. The present disclosure meets these andother challenges.

SUMMARY OF THE DISCLOSURE

The present disclosure comprises compositions and methods for assemblinggenetic pathways for expression in S. cerevisiae. The pathway assemblymethod, called VEGAS (Versatile Genetic Assembly System), exploits thenative capacity of S. cerevisiae to perform homologous recombination andefficiently join sequences with terminal homology. Terminal homologybetween adjacent pathway genes and an assembly vector is encoded by‘VEGAS adapter’ (VA) sequences, which are orthogonal in sequence withrespect to the yeast genome. Prior to pathway assembly by VEGAS in S.cerevisiae, each gene is assigned an appropriate pair of VAs andassembled using a technique called yeast Golden Gate (yGG). The VEGASimprovement enables building a plurality of transcription units (TUs).We demonstrate the assembly of four, five, and six gene pathways byVEGAS to generate S. cerevisiae cells synthesizing β-carotene andviolacein. Moreover, we demonstrate the capacity of the VEGAS approachfor combinatorial assembly. Thus, the disclosure in various embodimentsencompasses compositions and methods for making recombinant vectorssuitable for homologous recombination with each other in yeast.

In an embodiment the disclosure provides a method comprising: i)providing a first recombinant vector (CDS vector) comprising a proteincoding sequence (CDS sequence) wherein the CDS is flanked on its 5′ and3′ ends by first Type IIS restriction enzyme recognition sites, the CDSvector further comprising a first antibiotic resistance gene; ii)providing a second recombinant vector (PRO vector) comprising a promotersequence (PRO sequence) wherein the PRO sequence is flanked on its 5′and 3′ ends by the first Type IIS restriction enzyme recognition sites,the PRO vector further comprising the first antibiotic resistance gene;iii) providing a third recombinant vector (TER vector) comprising atranscription termination sequence (TER sequence) wherein the TERsequence is flanked on its 5′ and 3′ ends by the first restriction TypeIIS enzyme recognition sites, the TER vector further comprising thefirst antibiotic resistance gene; iv) providing a fourth recombinantvector (LVA vector) comprising a first left adapter polynucleotidesequence (LVA sequence) wherein the LVA sequence is flanked on its 5′and 3′ ends by the first Type IIS restriction enzyme recognition sites,the LVA vector further comprising the first antibiotic resistance gene;v) providing a fifth recombinant vector (RVA vector) comprising a firstright adapter polynucleotide sequence (RVA sequence) wherein the RVAsequence is flanked on its 5′ and 3′ ends by the first Type IISrestriction enzyme recognition sites, the RVA vector further comprisingthe first antibiotic resistance gene; vi) providing a sixth recombinantvector (acceptor vector) comprising a segment, the segment comprising apolynucleotide sequence encoding a detectable marker (detectable markersequence), wherein the detectable marker sequence is flanked by thefirst Type IIS restriction enzyme recognition sites, and wherein thesegment is flanked by a second Type IIS restriction enzyme recognitionsites, wherein the acceptor vector comprises a second antibioticresistance gene but does not comprise the first antibiotic resistancegene; vii) incubating the CDS vector, the PRO vector, the TER vector,the LVA vector, the RVA vector, and the acceptor vector in a singlereaction container with a first Type IIS restriction endonuclease thatrecognizes the first Type IIS restriction endonuclease recognition siteand a DNA ligase enzyme such that ligated vectors are produced, whereinthe ligated vectors comprise sequentially the LVA sequence, the PROsequence, the CDS sequence, the TER sequence, and the RVA sequence(LVA-TU-RVA vectors), wherein the PRO, CDS and TER sequences comprise atranscription unit (TU), and wherein the LVA-TU-RVA vectors comprise thesecond antibiotic resistance gene, but do not comprise the firstantibiotic resistance gene, wherein the LVA-TU-RVA vectors do notcomprise the detectable marker sequence, and wherein the ligated vectorsdo not comprise the first Type IIS restriction site, but do comprise thesecond Type IIS restriction site; viii) introducing the LVA-TU-RVAvectors from vii) into bacteria and culturing the bacteria with aculture medium comprising an antibiotic to which bacteria comprising theLVA-TU-RVA vectors are resistant via expression of the second antibioticresistance gene such that clonal colonies of the bacteria comprising theVEGAS vectors are formed, wherein the clonal colonies do not express thedetectable marker; and viii) isolating the LVA-TU-RVA vectors from thecolonies that do not express the detectable marker to obtain isolatedLVA-TU-RVA vectors. In embodiments, certain steps of the method areperformed using PCR. In certain embodiments, the CDS sequence compriseson its 5′ end the sequence: AATG and at its 3′ end the sequence TGAG;and/or the PRO sequence comprises at its 5′ end the sequence: CAGT andat its 3′ end the sequence AATG; and/or the TER sequence comprises atits 5′ end the sequence TGAG and at its 3′ end the sequence TTTT; and/orthe LVA sequence comprises at its 5′ end the sequence CCTG and at its 3′end the sequence CAGT; and/or the RVA sequence comprises at its 5′ endTTTT and at its 3′ end the sequence AACT; and/or the detectable markersequence comprises at its 5′ end the sequence CCTG and at its 3′ end thesequence AACT.

In certain embodiments, the disclosure includes a first LVA sequencethat comprises or consists of the sequence:CCCCTTAGGTTGCAAATGCTCCGTCGACGGGATCTGTCCTTCTCTGCCGGCGATCGT (SEQ ID NO:1)(VA1*). In certain embodiments, the disclosure includes a first RVAsequence that comprises or consists of the sequence:

(VA2**) (SEQ ID NO: 2) TGACGCTTGGATGCGTGACCCCGTACGTCATGACCCGTCATGGGTATGTAAGCGAAG.

In an aspect of the disclosure a method for producing a homologouslyrecombined DNA molecule comprising distinct transcription units (TU) isprovided. This generally comprises: i) providing a plurality ofLVA-TU-RVA vectors obtained as described above, wherein each LVA-TU-RVAvector in the plurality comprises a distinct TU that comprises adistinct CDS, and wherein each LVA-TU-RVA vector further comprises anLVA sequence and an RVA sequence, wherein only one LVA-TU-RVA vector inthe plurality comprises a first LVA sequence (VA1 sequence) that isidentical to a first LVA sequence in a yeast VEGAS acceptor vector, andwherein only one LVA-TU-RVA vector in the plurality comprises a firstRVA sequence (VA2 sequence) that is identical to a first RVA sequence inthe yeast VEGAS acceptor vector. The method further comprises ii)linearizing the plurality of LVA-TU-RVA vectors by digestion with a TypeIIS restriction enzyme to obtain distinct linearized LVA-TU-RVA vectorfragments that comprise the distinct TUs, and sequentially orconcurrently iii) providing a linearized yeast VEGAS acceptor vectorthat comprises at one end the VA1 sequence and at the other end the VA2sequence, the linearized yeast VEGAS acceptor vector further comprisinga sequence encoding selectable marker functional in bacteria, aselectable marker functional in yeast, a yeast centromere (CEN)sequence, and a yeast autonomously replicating sequences (ARS). Themethod further comprises iv) introducing into the yeast the linearizedyeast VEGAS acceptor vector and the distinct linearized LVA-TU-RVAvector fragments that comprise the distinct TUs. After introduction ofthese components the method comprises v) allowing homologousrecombination in the yeast so that the only one LVA-TU-RVA vectorsegment comprising the VA1 sequence and the only one LVA-TU-RVA vectorsegment comprising the VA2 sequence are homologously recombined with thelinearized yeast VEGAS acceptor vector to form circularized doublestranded DNA polynucleotides comprising at least the two distinct TUs.The method also optionally comprises isolating the circularized doublestranded DNA polynucleotides from the yeast. In embodiments, thedisclosure includes a plurality of LVA-TU-RVA vectors that comprises atleast one, two, three or four additional distinct LVA-TU-RVA that arehomologously recombined into a contiguous polynucleotide in yeast.

In embodiments the disclosure comprises yeast cells comprising ahomologously recombined DNA molecule made by a process described herein.Compositions comprising homologously recombined DNA molecules isolatedfrom the yeast cells are included, as the isolated recombined DNAmolecules themselves. Kits comprising polynucleotides for performing oneor more methods of the disclosure are included, and can further comprisereagents for digesting, ligating, isolating, purifying, transforming ortransfecting yeast. The kits can further comprise printed materialproviding instructions for carrying out any embodiment(s) of thedisclosure.

BRIEF DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1. One-pot yGG assembly. PRO, CDS, and TER parts flanked by theappropriate prefix and suffix sequences are cloned into kanamycinresistant vectors. For ‘one-pot’ digestion-ligation reaction clonedparts are mixed in equimolar ratio with ampicillin resistant “acceptorvector” for subsequent yGG assembly of TUs. The parental acceptor vectorencodes a red fluorescent protein (RFP) gene with E. coli promoter andterminator sequences. Following E. coli transformation, white/redscreening can be used to distinguish clones encoding putative TUassemblies as compared to unmodified parental vector.

FIG. 2. yGG acceptor vectors. (A) Schematic representation of acceptorvector nomenclature. (B) Schematic of representative acceptor vectors.All yGG acceptor vectors (AVs) encode resistance to ampicillin (AMP^(R))or chloramphenicol (not pictured) to permit construction of TUs in a‘one-pot’ reaction with PRO, CDS, and TER parts that are cloned intokanamycin resistant vectors. Following transformation of yGG reactionproducts into E. coli, white/red screening can be used to identifyclones encoding assembled constructs.

FIG. 3. Efficiency of yGG with different numbers of Parts. 4 part and 8part yGG assembly was performed in the presence of 10 U, 10 U and 100 Uof BsaI with a volume of 1 μl, 0.1 μl and 1 μl of enzyme respectively.The yGG reaction products were transformed into bacteria and plated onLB-Carb plates. Pictures were taken after 1 day's incubation at 37° C.White and red colonies were counted; white colonies percentage isindicated on the lower right of the picture. The fraction on the lefthand side is the amount of correct assembly clones, as measured byplasmid prep and digest of 12 white colonies.

FIG. 4. yGG to construct a TU encoding a C-terminally tagged CDS. (A)The CDS is part flanked by the appropriate prefix and suffix sequencesand cloned into a kanamycin resistant vector (Supplementary Data). Priorto TU assembly by yGG, the CDS construct is digested with BceAI andsubsequently gel purified. The BceAI digested CDS fragment is mixed withPRO, TER, Long Tag (e.g. GFP, mCherry, TAP, GST) constructs, eachflanked by the appropriate prefix and suffix sequences, plus Short Tag(e.g. flag, V5, HA etc.) or linker annealed oligos and desired yGGacceptor vector. The mixture is then subjected to a ‘one-pot’digestion-ligation reaction with the appropriate enzymes to assemble thetagged TU. Following E. coli transformation, white/red screening can beused to distinguish clones encoding putative TU assemblies as comparedto unmodified parental vector. (B) Colony PCR was performed on 13 whitecolonies from yGG assembly carried out as described in (A). Primersamplified a region around the C-terminus of the V5-GFP tagged protein todifferentiate tagged and untagged clones. 10 of 13 amplicons areconsistent with the predicted size for the tagged construct. C=untaggedconstruct, M=DNA ladder. (C) Functional validation of C-terminallytagged HTP1. HTP1 C-terminally tagged with GFP or mCherry is functional,thus cells grow on medium containing hypoxanthine as the sole purinesource. HPRT, the human ortholog of HPT1 and known to functionallycomplement is a positive control. Fluorescence microscopy revealsexpression of both mCherry and GFP in these cells.

FIG. 5. Elimination of a BsaI site using yGG. Schematic representationof the design of parts in order to eliminate a BsaI restriction site toenable one-pot assembly using yGG. For a BsaI site oriented to cutupstream of its recognition site, two primers should overlap the site;one reverse primer (Reverse primer 1) that will amplify the sequenceupstream (Fragment 1) and will include the recognition site. The secondprimer (Forward Primer 2) will amplify the sequence downstream (Fragment2), mutate the original restriction site (mutated site marked in red)oriented to create a complementary overhang to the upstream fragment.Following yGG the product will have no BsaI recognition site.

FIG. 6. Yeast Golden Gate (yGG) to assemble transcription units flankedby VEGAS adapters. (A) yGG reactions to build transcription units (TUs)destined for VEGAS pathway assembly in S. cerevisiae include 5 parts: aleft VEGAS adapter (LVA), a promoter (PRO), a coding sequence (CDS), aterminator (TER), and a right VEGAS adapter (RVA). Each part is flankedby inwardly facing recognition sequences for the BsaI restrictionenzyme, an “offset cutter” which cuts outside its recognition sequence(at positions 1/5 bp downstream) to expose the indicated 4 base-pairoverhangs. All parts are cloned into vectors encoding kanamycinresistance (KAN^(R)) and an E. coli replication origin (Ori). (B) TheyGG acceptor vector for VEGAS is designed such that outwardly facingBsaI sites expose overhangs corresponding to the 5′ LVA and 3′ RVAoverhangs to promote assembly of the TU in the vector during a one-potrestriction-digestion reaction. The RFP cassette, built for expressionin E. coli, is cut out of the vector when a TU correctly assembles,enabling white-red screening. The yGG acceptor vector encodes resistanceto ampicillin (AMP^(R)) (C) The structure of a VA-flanked TU assembledby yGG. An assembled TU plus the flanking VA sequences may be releasedfrom the yGG acceptor vector by digestion with BsmBI.

FIG. 7. VEGAS vector for pathway assembly. Digestion with BsaIlinearizes the VEGAS assembly vector, releasing an RFP cassette andexposing terminal VA sequences VA1 and VA2 on the vector arms. Assemblyof a genetic pathway by homologous recombination in yeast is selected onmedium lacking uracil based on expression of URA3 from the vectorbackbone and mitotic stability in dividing yeast cells ensured based onthe centromere (CEN) and autonomously replicating sequence (ARS)combination encoded on the vector. The VEGAS assembly vector alsoencodes resistance to ampicillin (AMP^(R)) plus an E. coli replicationorigin (Ori); assembled constructs can therefore be recovered from yeastinto E. coli.

FIG. 8. VEGAS with adapter homology to assemble a five gene pathway. (A)The pathway consisting of VA-flanked TUs assembled by yGG may bereleased in one piece from the yGG acceptor vector by digestion withBsmBI (scissors). (B) A genetic pathway may be assembled into thelinearized VEGAS assembly vector in S. cerevisiae by homologousrecombination between VAs that flank TUs (TU1-5). X's indicatehomologous recombination.

FIG. 9. FIG. 4. VEGAS with PCR-mediated homology to assemble a four genepathway. (A) TUs flanked by unique VAs are assembled by yGG and thensubjected to PCR using primers that introduce terminal homology betweenadjacent parts. In this example, the reverse primer amplifying TU1encodes 30 bp of sequence homology to VA4 and the forward primeramplifying TU2 encodes 30 bp of sequence homology to VA3. Together thisgenerates 60 bp of terminal sequence homology between TU1 and TU2 forthe homologous recombination machinery in S. cerevisiae to assemble alinear piece of DNA in vivo. (B) Gene order may be changed by usingdifferent overhang primers; here the final pathway structure becomesTU1-TU3-TU4-TU2, although any order and/or gene orientation is possibleand depends only on primer design.

FIG. 10. VEGAS with adapter homology to assemble the carotenoid pathwayin S. cerevisiae. (A) The four β-carotene pathway genes (crtE, crtI,crtYB, tHMG1), assembled as TUs flanked by the indicated VAs (see Table4 for PRO and TER parts) were released from the yGG acceptor vector withBsmBI digestion and co-transformed into yeast with the linearized VEGASassembly vector. (B) S. cerevisiae colonies encoding assembled pathwaysdevelop a bright yellow color on medium lacking uracil (SC-Ura; leftpanel) as well as on YPD medium supplemented with G418 (right panel).

FIG. 11. VEGAS with PCR-mediated homology to assemble the β-carotene andviolacein pathways in S. cerevisiae. (A) The four β-carotene pathwaygenes (crtE, crtI, crtYB, tHMG1), assembled as TUs flanked by theindicated VAs (see Table 5 for PRO and TER parts) were subjected to PCRusing primers to generate adjacent terminal homology between TUs and theVEGAS assembly vector. (B) S. cerevisiae colonies encoding assembledpathways develop a bright yellow color on medium lacking uracil (SC-Ura;left panel) as well as on YPD medium supplemented with G418 (rightpanel). (C) Re-streaked single colonies from three VEGAS assemblyexperiments. Left panel: A single yellow colony from the VEGAS assemblyexperiment in (B) was re-streaked for single colonies. Right panel: bydesigning a few new primers, a second version of the carotenoid pathwaywas assembled omitting the tHMG1 TU, generating orange yeast colonies.(D) The violacein pathway assembled in S. cerevisiae yields purplecolonies.

FIG. 12. Combinatorial assembly of the β-carotene pathway in S.cerevisiae. (A) Combinatorial TU libraries of the four β-carotenepathway genes (crtE, crtI, crtYB and tHMG1), were generated by yeastGolden Gate and assembled for expression in yeast by VEGAS as in FIG. 11except with pools of 10 PRO and 5 TER parts for each yGG assembly ofeach TU. Transformants of varying colors reflect production of differentlevels of 3-carotene and its intermediates due to varied expression ofall genes in the pathway leading to different concentrations of both endproduct and intermediates. (B and C). Single colony purification oftransformants in (A). (D-H). Five assembled constructs were recoveredfrom yeast into E. coli (pJC175, pJC178, pJC181, pJC184, and pJC187) andsequenced to identify the promoters and terminators driving expressionof each pathway gene. Each construct was also re-transformed into yeastto verify production of β-carotene (and intermediates) based on theyeast colonies developing color uniformly. Shown are replica plates onYPD supplemented with G418. (I). HPLC quantification of carotenoidsproduced in strains FIG. 12E-H. In all cases ˜12.5 g of yeast (dry cellweight (DCW)) was used for the analysis. Quantification was performed inbiological triplicate for each strain as shown. All strains analysedcontained additional carotenoid peaks that may have contributed to colorformation.

DESCRIPTION OF THE DISCLOSURE

The present disclosure is related to improved compositions and methodsthat are useful for assembling sets of genes for expression in cells. Avariety of cell types cells can be modified and used according toembodiments of this disclosure, provided the cells have the ability topromote homologous recombination, whether endogenously or having beenengineered to facilitate homologous recombination. In embodiments, thecells are eukaryotic cells. In embodiments, the eukaryotic cells aresingle-celled organisms. In embodiments, the single-celled eukaryoticorganisms are members of the taxonomic kingdom Fungi. In embodiments theorganisms are Ascomycota. In embodiments, the organisms are the membersof Saccharomyces, Kluyveromyces, Pichia, Candida, Aspergillus,Penicillium, Fusarium, Claviceps, Schizosaccharomyces, Hansenula,Sordaria, Neurospora, or Fusarium. In embodiments, the single-celledeukaryotic organisms comprise yeasts or molds. Non-limiting embodimentsof this disclosure are illustrated using S. cerevisiae.

In particular, the disclosure encompasses what is referred to as aVersatile Genetic Assembly System (VEGAS), thus providing a new methodto construct genetic pathways for expression in eukaryotic cells, suchas S. cerevisiae. The disclosure includes assembly of a plurality ofgenes, or transcription units (TUs), using modifications of theso-called Golden Gate approach, and combines a yeast-specific GoldenGate approach referred to herein as yeast Golden Gate (yGG) withhomologous recombination performed in yeast, yielding the VEGAS aspectof the disclosure. In the VEGAS aspect, each TU is assigned a pair ofVEGAS adapters that assemble up- and downstream of each TU; it is theVEGAS adapter sequences that subsequently provide terminal homology foroverlap-directed assembly by homologous recombination ‘in yeasto’. Asproof of principle, we apply the VEGAS methodology to the assembly ofthe β-carotene and violacein biosynthetic pathways, whose pigmentedproducts are visible in yeast colonies. Moreover we demonstrate thecapacity of VEGAS for combinatorial assembly, thus creating thepotential to assemble a wide variety of TUs that can impart to the yeastthe capability to perform myriad functions.

This disclosure comprises but is not limited to every polynucleotidesequence described in the accompanying sequence listing, as well as eachpolynucleotide sequence presented in the text, and those depicted in theFigures. The disclosure includes fragments of each of thesepolynucleotide sequences, wherein the fragments contain at least 4contiguous nucleotides of any of the polynucleotide sequences. Eachpolynucleotide sequence disclosed herein includes its complementarysequence. Thus, every sequence provided in the 5′-3′ orientation isconsidered to include a description of the complementary 3′-5′ sequence,and vice versa. For every polynucleotide sequence disclosed hereindouble stranded and single stranded polynucleotides are included, as arepolynucleotides that are only partially double stranded, such as apolynucleotide having a single-stranded overhang that is created by, forexample, digestion with a Type IIS restriction enzyme. Single strandedoverhangs include those having a 3′ or a 5′ terminal nucleotide. Kitscomprising any one or any combination of the polynucleotides describedherein are included in the disclosure. The kits can include any one orany combination of the vectors described herein, primers, restrictionenzymes, a ligase, suitable buffers for one-pot restriction digestionand ligase reactions, reagents for introducing linear DNA molecules intoyeast, and reagents for separating vectors or other polynucleotides ofthis disclosure from cell cultures, and/or for purifying such vectors orother polynucleotides. In embodiments the kits comprise reagents for usein assembling a set of genes for heterologous expression in yeast,wherein at least some members of the set of genes encode proteins thatcooperate in one or more biosynthetic pathway(s), wherein expression ofthe proteins is necessary, and may be necessary and sufficient, for theproduction of a particular product. The product can be any product thatcan be synthesized by yeast modified according to this disclosure and isnot particularly limited. Some non-limiting examples of such productsinclude carotenoids, such as beta-carotene, phyotene, lycopene, andviolacein. The disclosure also includes but is not limited to synthesisof classes of pharmacologically active compounds, such as polyketides,non-ribosomal peptides, terpenes, carbohydrates, and derivatives oftryptophan and other amino acids. Thus, the disclosure comprises thesynthesis of any substance, molecule, compound or complex that can bemade by a cell expressing a plurality of genes via the presentlyprovided approaches.

In one aspect the disclosure generally comprises compositions andmethods for making recombinant vectors suitable for homologousrecombination with each other in unicellular micyeast, and furthercomprises facilitating the homologous recombination to produce apolynucleotide comprising a plurality of transcription units. Inembodiments, the disclosure includes polynucleotides that comprise apromoter sequence, a coding sequence, and a transcription terminationsequence, which collectively comprise a transcription unit (TU). In anembodiment a method of the disclosure comprises: i) providing a firstrecombinant vector (CDS vector) comprising a protein coding sequence(CDS sequence) wherein the CDS is flanked on its 5′ and 3′ ends by firstType IIS restriction enzyme recognition sites, the CDS vector furthercomprising a first antibiotic resistance gene; ii) providing a secondrecombinant vector (PRO vector) comprising a promoter sequence (PROsequence) wherein the PRO sequence is flanked on its 5′ and 3′ ends bythe first Type IIS restriction enzyme recognition sites, the PRO vectorfurther comprising the first antibiotic resistance gene; iii) providinga third recombinant vector (TER vector) comprising a transcriptiontermination sequence (TER sequence) wherein the TER sequence is flankedon its 5′ and 3′ ends by the first restriction Type IIS enzymerecognition sites, the TER vector further comprising the firstantibiotic resistance gene; iv) providing a fourth recombinant vector(LVA vector) comprising a first left adapter polynucleotide sequence(LVA sequence) wherein the LVA sequence is flanked on its 5′ and 3′ endsby the first Type IIS restriction enzyme recognition sites, the LVAvector further comprising the first antibiotic resistance gene; v)providing a fifth recombinant vector (RVA vector) comprising a firstright adapter polynucleotide sequence (RVA sequence) wherein the RVAsequence is flanked on its 5′ and 3′ ends by the first Type IISrestriction enzyme recognition sites, the RVA vector further comprisingthe first antibiotic resistance gene; vi) providing a sixth recombinantvector (acceptor vector) comprising a segment, the segment comprising apolynucleotide sequence encoding a detectable marker (detectable markersequence), wherein the detectable marker sequence is flanked by thefirst Type IIS restriction enzyme recognition sites, and wherein thesegment is flanked by a second Type IIS restriction enzyme recognitionsites, wherein the acceptor vector comprises a second antibioticresistance gene but does not comprise the first antibiotic resistancegene; vii) concurrently incubating the CDS vector, the PRO vector, theTER vector, the LVA vector, the RVA vector, and the acceptor vector,such as in a single reaction container, with a first Type IISrestriction endonuclease that recognizes the first Type IIS restrictionendonuclease recognition site and a DNA ligase enzyme such that ligatedvectors are produced, wherein the ligated vectors comprise sequentiallythe LVA sequence, the PRO sequence, the CDS sequence, the TER sequence,and the RVA sequence (LVA-TU-RVA vectors), wherein the PRO, CDS and TERsequences comprise a transcription unit (TU), and wherein the LVA-TU-RVAvectors comprise the second antibiotic resistance gene, but do notcomprise the first antibiotic resistance gene, wherein the LVA-TU-RVAvectors do not comprise the detectable marker sequence, and wherein theligated vectors do not comprise the first Type IIS restriction site, butdo comprise the second Type IIS restriction site; viii) introducing theLVA-TU-RVA vectors from vii) into bacteria and culturing the bacteriawith a culture medium comprising an antibiotic to which bacteriacomprising the LVA-TU-RVA vectors are resistant via expression of thesecond antibiotic resistance gene such that clonal colonies of thebacteria comprising the VEGAS vectors are formed, wherein the clonalcolonies do not express the detectable marker; and viii) isolating theLVA-TU-RVA vectors from the colonies that do not express the detectablemarker to obtain isolated LVA-TU-RVA vectors. In certain embodiments,the disclosure comprises C-terminally tagged TUs as described furtherbelow. In certain embodiments, oligonucleotides can be substituted forvectors or vector parts, or can be used in combination with the vectorsof this disclosure, as also described further below.

With respect to the parts of the vectors that are encompassed by thisdisclosure, the PRO sequence can be any suitable eukaryotic promoterthat can facilitate transcription of the CDS sequence in yeast. In thisregard, many promoter sequences that can drive transcription in yeastare known in the art. For example, the Promoter Database ofSaccharomyces cerevisiae (SCPD) includes promoter regions forapproximately 6,000 yeast genes, and also includes regulatory elementsand transcription factors that can also be taken into account whenapproaching various aspects of this disclosure if desired. The SPCD canbe accessed via rulai.cshl.edu/SCPD/. In embodiments, the promoter is aconstitutively active promoter or an inducible promoter. In embodimentsthe promoter is a strong promoter, a medium promoter, a weak promoter,or a minimal promoter. In embodiments the promoter is not native to theyeast genome, and is inducible by the presence/absence of a smallmolecule, such as a tet-inducible promoter. Combinations of distinctpromoters can be used with different TUs to achieve, for example, adesired stoichiometry of RNA and/or protein products when transcriptionis driven by the distinct promoters. In embodiments, the PRO drivestranscription of RNA Polymerase II.

The CDS can be any sequence that is transcribed into RNA. Inembodiments, the CDS encodes a peptide, polypeptide or protein. Thoseskilled in the art will recognize that any peptide, polypeptide orprotein can be encoded by the CDS and, given an appropriate promoter incommunication with the CDS, can be expressed in yeast. Thus, the CDS cancomprise one or more open reading frames (ORFs). The CDS can encode incertain embodiments, an enzyme, or a structural protein, or a receptor,a ligand for a receptor, a peptide hormone, a binding agent such as anantibody or fragment thereof, a protein that binds one or more compoundssuch as for storage or transport, a transcription factor or other DNA orRNA binding protein, a contractile protein, or any other type ofprotein. Alternatively, the CDS can encode an RNA that is not an mRNA.For example, the CDS could encode an RNA that has a regulatory or otherfunction. In embodiments, the CDS encodes an RNA that is capable ofparticipating in RNAi mediated degradation of a target RNA, and canaccordingly comprise an siRNA, an shRNA, a microRNA, or a ribozyme. Inembodiments, the CDS encodes a Small nucleolar RNA (snoRNAs), a guideRNA or trans-activating crRNA (tracrRNA), such as for use with aCRISPR-based DNA editing system. In embodiments, the RNA encoded by theCDS can comprise a tRNA, an rRNA, or another RNA that can form acomponent of a Ribonucleoprotein (RNP).

The TER sequence can comprise any suitable transcription terminationsequence which functions to designate a location on the transcriptiontemplate where the RNA polymerase is released from transcription inyeast. In embodiments, the TER sequence can comprise or is immediatelyjuxtaposed to a polyadenylation signal. In embodiments, the TER isfollowed by TTTT or AAAA. In embodiments, the TTTT or AAAA is present ina single-stranded overhang. Further, a variety of suitable terminationsignals are known in the art (i.e., Guo Z and Sherman F., 3′-end-formingsignals of yeast mRNA. Trends Biochem Sci. 1996 December; 21(12):477-81;and Curran, K. et al., Short Synthetic Terminators for ImprovedHeterologous Gene Expression in Yeast. ACS Synth. Biol. DOI:10.1021/sb5003357).

The Type IIS restriction enzymes and their recognition sites are allwell known in the art. In embodiments, the disclosure includes pairs ofType IIS restriction sites that flank certain segments of vectors asdescribed further below. In embodiments, the Type IIS restriction sitescan be inwardly facing with respect to the segment they flank. Thisconfiguration is illustrated, for example FIG. 1, in which the topvector includes a pair of inwardly facing BsaI sites that flank the CDS.The sequence AATG sequence shown after the BsaI site illustrates asingle stranded overhang that would be left after cleavage using BsaI.It should be recognized that AATG sequence, and the sequence ACTC whichis depicted at the other end of the CDS, represent a specific prefix andsuffix sequence, respectively. These sequences are comprised withindesigned sequences that enable directional assembly of TUs via theinwardly facing Type IIS restriction sites with a 4 bp overhangseparated from the recognition sequence by a single base to accommodatethe offset cutting by the enzyme. These Type IIS sites can be orientedsuch that they are eliminated upon digestion, and which exposes thedesigned overhangs. Representative and non-limiting examples of prefixand suffix sequences that are suitable for use with the presentdisclosure are presented in Table 1, but others can be designed by thoseskilled in the art given the benefit of the present disclosure. Inembodiments, the disclosure also includes use of outwardly facing TypeIIS recognition sites. This configuration is illustrated in anon-limiting embodiment in the Acceptor Vector of FIG. 1, wherein theRed Fluorescent Protein (RFP) coding sequence is flanked by outwardlyfacing BsaI sites.

In embodiments, the disclosure includes using a second Type IISrestriction enzyme and its recognition sequence. For example, in anon-limiting embodiment, FIG. 6 depicts a VEGAS acceptor vector thatcomprises an RFP segment flanked by outwardly facing BsaI sites, andthat segment is itself flanked by inwardly facing BsmBI sites. It shouldbe recognized that reference to “first” and “second” Type IISrestriction enzymes and sites is for convenience and does notnecessarily specify order or preference. The same applies to the terms“first” and “second” etc. as used to describe other parts of embodimentsof this disclosure. It is considered that any other Type IIS restrictionendonucleases and their concomitant recognition sequences can be adaptedfor use in methods of this disclosure. For example, in embodiments, acombination of different Type IIS restriction enzymes and sites can beused in assembling a TU as described herein, so long as they can allfunction in the same reaction, and provided that the combination ofsites used in the CDS, PRO and TER vectors, for example, are not alsoencoded on the acceptor vector illustrated in Panel C of FIG. 6.

In embodiments, certain vectors and linearized polynucleotides encodeantibiotic resistance genes. A wide variety of antibody resistance genesare known in the art and can be used with embodiments of thisdisclosure. In one approach, two distinct antibiotic resistance genesare used. In one embodiment, a first antibiotic resistance genecomprises a kanamycin resistance gene. In an embodiment, a secondantibiotic resistance gene comprises an ampicillin resistance gene.

In embodiments, the vectors of this disclosure comprise shuttle vectors,and thus they comprise components that permit their propagation inprokaryotic and eukaryotic cells. In embodiments, the vectors compriseone or any combination of a prokaryotic origin of replication (Ori), anauxotrophic marker functional in yeast (i.e., URA3 or any of a widevariety of the other suitable autotrophic marker genes), and a sequencefacilitating episomal replication in yeast, such as acentromere/autonomously replicating sequence (CEN/ARS). Suitable CEN andARS sequences are well known in the art. Thus, in embodiments, thedisclosure comprises a plurality of distinct TUs in a vector that ismaintained episomally in yeast, and yeast comprising such episomalelements. In certain embodiments, the disclosure includes vectors thatare adapted for integration into a yeast chromosome, and thus do notcomprise CEN/ARS sequences. Representative and non-limiting examples ofsuch acceptor vectors designed for integration into the URA3, LEU2,TRP1, and HIS3 loci are shown in FIG. 2. The disclosure thus encompassesintegration of a plurality of TUs into a yeast chromosome, and yeastcomprising such integrations. The disclosure accordingly includesintegrative acceptor vectors (FIG. 2) that comprise a polynucleotidesequence that is homologous to an innocuous site in the yeast genome.Non-limiting examples of such sites include the HO locus on chromosome4, intergenic regions on the left arm of chromosome 6 and right arm ofchromosome 9, and a dubious ORF on chromosome 11 (YKL162C-A) (see Table2).

In one embodiment a vector used in the disclosure encodes a detectablemarker. In general, the marker can be (but does not necessarily need tobe) a visually detectable marker, such as a protein that participates inthe production of a color that is visually perceptible by a human. Inthis regard, red fluorescent protein (RFP) is used to facilitateselection of bacteria that contain properly assembled vectors, and assuch they do not express RFP due to excision of its coding sequence fromthe properly assembled constructs. However, a detectable marker couldalso be configured to identify properly assembled constructs via itsexpression. Thus, there are a variety of detectable markers andconfigurations of them that can be implemented in various approaches tofacilitate isolation of properly assembled constructs, and thesealternative approaches will be apparent to those skilled in the artgiven the benefit of the present disclosure.

In embodiments, vectors of this disclosure comprise VEGAS adaptersequences. The VEGAS adapter sequences are referred to as “left” and“right” simply to illustrate their position relative to the sequentialPRO, CDS, TER orientation of the vectors as will be readily apparentfrom the Figures of this description. The left and right VEGAS adaptersare from time to time referred to as LVA and RVA, respectively, in thisdisclosure. The VEGAS adapter sequences are orthogonal to the yeastgenome, and thus, in certain embodiments, a VEGAS sequence is not partof the genome of yeast into which a vector comprising the VEGAS adaptersequence is introduced. This is intended to preclude inadvertentrecombination with the yeast chromosome, but it will be recognized thatthe disclosure does not exclude intentionally designed recombinationwith a yeast chromosome as described further below. The VEGAS adaptersparticipate in combinatorial and sequence oriented recombination oflinearized vectors as illustrated generally in FIG. 8. The VEGASadapters of this disclosure comprise or consist of 35-500 base pairs(bp), inclusive, and including all integers there between and all rangesof integers there between, with the proviso that the adapters are: a)less than 90% identical to any contiguous sequence in the genome of thecell type into which they are introduced, such as a yeast, wherein theless than 90% range includes all integers including and between 90% and0% identity, including all ranges of integers there between, and incertain embodiments are less than 50% identical to the genome of thereceiving cell; b) orthogonal to each other, meaning the LVA and RVA onthe same vector are less than 90% identical to each other, wherein theless than 90% range includes all integers including and between 90% and0% identity, including all ranges of integers there between, and incertain embodiments are less than 50% identical to the each other,wherein the identity is applied either between VA pairs, or for all VAsused in any particular situation, and c) comprise greater than 30% GCcontent and less than 70% GC continent in base composition; thus, theVAs in certain embodiments comprise from 30% to 70% GC content,inclusive, and including all digits and ranges of digits there between.The disclosure includes representative and non-limiting VEGAS adaptersequences that are presented in Table 3. In embodiments, a vectorcomprising an LVA, a TU and an RVA is referred to herein as an“LVA-TU-RVA” vector.

In embodiments, the disclosure provides vectors which comprise partsselected from: a CDS sequence that comprises on its 5′ end the sequence:AATG and at its 3′ end the sequence TGAG; a PRO sequence that comprisesat its 5′ end the sequence: CAGT and at its 3′ end the sequence AATG; aTER sequence that comprises at its 5′ end the sequence TGAG and at its3′ end the sequence TTTT; an LVA sequence that comprises at its 5′ endthe sequence CCTG and at its 3′ end the sequence CAGT; an RVA sequencethat comprises at its 5′ end TTTT and at its 3′ end the sequence AACT;and in certain cases, a detectable marker sequence that comprises at its5′ end the sequence CCTG and at its 3′ end the sequence AACT. In certainembodiments, the disclosure includes a first LVA sequence that comprisesor consists of the sequence:

(VA1*) (SEQ ID NO: 1) CCCCTTAGGTTGCAAATGCTCCGTCGACGGGATCTGTCCTTCTCTGCCGGCGATCGT.

In certain embodiments, the disclosure includes a first RVA sequencethat comprises or consists of the sequence:

(VA2**) (SEQ ID NO: 2) TGACGCTTGGATGCGTGACCCCGTACGTCATGACCCGTCATGGGTATGTAAGCGAAG.

In an aspect the disclosure includes producing a homologously recombinedDNA molecule comprising distinct TUs described above. The method in oneembodiment comprises providing a plurality of LVA-TU-RVA vectors,wherein each LVA-TU-RVA vector in the plurality comprises a distinct TUthat comprises a CDS, and wherein each LVA-TU-RVA vector furthercomprises an LVA sequence and an RVA sequence, wherein only oneLVA-TU-RVA vector in the plurality comprises the first LVA sequence(referred to as a “VA1 sequence”) that is identical to a first LVAsequence in a yeast VEGAS acceptor vector, and wherein only oneLVA-TU-RVA vector in the plurality comprises a first RVA sequence(referred to as a “VA2 sequence”) that is identical to a first RVAsequence in a yeast VEGAS acceptor vector. The plurality of theLVA-TU-RVA vectors is linearized by digestion with a Type IISrestriction enzyme that recognizes a Type IIS restriction site, thusyielding distinct linearized LVA-TU-RVA vector fragments that comprisethe distinct TUs. The method further comprises providing a linearizedyeast VEGAS acceptor vector that comprises at one end the VA1 sequenceand at the other end the VA2 sequence, the linearized yeast VEGASacceptor vector further comprising a sequence encoding selectable markerfunctional in bacteria, a selectable marker functional in yeast, a yeastCEN sequence, and an ARS sequence. The method comprises introducing intothe yeast the linearized yeast VEGAS acceptor vector and the distinctlinearized LVA-TU-RVA vector fragments that comprise the distinct TUs,and allowing homologous recombination in the yeast so that the only oneLVA-TU-RVA vector segment comprising the VA1 sequence and the only oneLVA-TU-RVA vector segment comprising the VA2 sequence are homologouslyrecombined with the linearized yeast VEGAS acceptor vector to formcircularized double stranded DNA polynucleotides comprising at least thetwo distinct TUs. Optionally, the method further comprises isolating thecircularized double stranded DNA polynucleotides from the yeast. Incertain embodiments, this approach provides a single polynucleotide thatcomprises two, three, four, five, or six, or more, TUs. Certain steps ofthis approach are illustrated in FIG. 8, which also illustrates anapproach to configuring the LVA and RVA sequences such that they arerecombined in the yeast in a predetermined order that is dictated atleast in part by the homology of the distinct LVA and RVA sequences. Inparticular, as will be evident from FIG. 8, the disclosure includesproviding an RVA sequence on one linearized vector that is the same asan LVA sequence on a distinct linearized vector to enable the yeast tohomologously recombine the two vectors into a contiguous polynucleotide.The approach can be repeated iteratively using different LVA and RVAsequences on distinct linearized vectors to assemble intentionallyordered TUs, as illustrated in FIG. 8.

Example 1

This Example provides an illustration of the construction of TUs forexpression in S. cerevisiae using a yeast Golden Gate (yGG) approachthat is modified in Example 2 to include the VEGAS adapter-basedapproach.

As described above, a TU used in this disclosure contains three parts: aUAS/promoter/5′UTR (PRO), a coding sequence (CDS), and a3′UTR/polyadenylation signal/terminator (TER). To enable directionalassembly of TUs we assign specific prefix and suffix sequences to eachof the three parts that encode “inwardly facing” Type IIS restrictionsites, typically BsaI or BsmBI, and a 4 bp “designer overhang” separatedfrom the recognition sequence by a single base to accommodate the offsetcutting by the enzyme (Table 1). These Type IIS RE sites are orientedsuch that they are eliminated upon digestion, exposing designeroverhangs as follows: 5′-CAGT-PRO-AATG-3′,5′-AATG-CDS-TGAG-3′, and5′-TGAG-TER-TTTT-3′, respectively (FIG. 1). (Note that all overhangs arelisted here as top strand sequences for clarity, but are the bottomstrands are given in certain instances in the Figures.) The overhangsselected are known to be highly compatible with regulated geneexpression and represent the smallest possible scars as they exploit thenatural punctuation marks ATG and TGA. Specifically, the AATG overhangbetween the PRO and CDS provides the ATG start codon. This overhangprovides a favorable context for gene expression, as most well-expressedyeast genes have their ATG initiation codons preceded by one or moreA's. Additionally, the TGAG overhang at the CDS/TER junction provides auniversal TGA stop codon. PRO, CDS, and TER parts flanked by theappropriate prefix and suffix sequences are cloned into, for example,kanamycin resistant vectors that do not encode genetic information forreplication in yeast. The subsequent yGG assembly of TUs is performedusing, for example, an ampicillin resistant “acceptor vector” in a‘one-pot’ digestion-ligation reaction as described further below. Theparental acceptor vector encodes detectable marker, such as a redfluorescent protein (RFP) gene with E. coli promoter and terminatorsequences. Thus, in this embodiment, following E. coli transformation,white/red colony color screening can be used to distinguish clonesencoding putative TU assemblies from those containing unmodifiedparental vector.

Acceptor Vectors.

We have constructed a series of illustrative acceptor vectors withmultiple markers and applications for use in vector assembly (Table 2).To facilitate TU assembly, acceptor vectors lack, for example, BsaIand/or BsmBI restriction sites except for two outwardly facing sitesflanking the RFP cassette described above. The overhangs generatedfollowing BsaI (or BsmBI) digestion are compatible with receiving the 5′overhang of the PRO part (CAGT) and the 3′ overhang of the TER part(TTTT). Subsequent to assembly, these vectors permit directtransformation of TUs into yeast cells.

The first two sets of yGG acceptor vectors are intended for independentreplication and segregation once transformed into S. cerevisiae andderive from the well-known pRS series of yeast shuttle vectors pRS41Xand pRS42X. These vectors encode either a centromere/autonomouslyreplicating sequence (CEN/ARS) combination (pRS41X; single copy) or 2micron parts (pRS42X; high copy), in addition to a selectable marker foryeast, plus selection and replication parts for bacteria (ampicillinresistance and a replication origin; FIG. 2).

The third type of acceptor vector is intended for integration into aspecific locus in the yeast genome and therefore lacks genetic partsthat enable independent replication in yeast (e.g. CEN/ARS or 2 micronsequences). To this end, as with the other two sets of pRS vectors wehave converted the pRS40X series into yGG TU acceptor vectors forintegration into the URA3, LEU2, TRP1, and HIS3 loci (FIG. 2).Furthermore, we have designed and built a series of custom integrativeacceptor vectors (FIG. 2). Here, a yeast selectable marker is encoded onone side of the BsaI-RFP-BsaI cassette, and together these parts areflanked by ˜500 bp regions targeting an innocuous site in the yeastgenome. These sites include the HO locus on chromosome 4, intergenicregions on the left arm of chromosome 6 and right arm of chromosome 9,and a dubious ORF on chromosome 11 (YKL162C-A) (Table 2). To facilitateintegration, on either side of the targeting sequences each customintegrating acceptor vector encodes rare cutting restriction sites suchas BciVI and/or NotI (Table 2). Digestion with the second enzyme canexcise the entire integration cassette, generating a substrate forrecombination with the corresponding endogenous locus in the yeastchromosome.

Designing and Constructing PRO, CDS, and TER Parts.

The boundaries of PRO, CDS, and TER parts are determined using rulesthat enable the automated extraction of their sequences from the yeastgenome (or elsewhere). Because the start and stop codon of a CDS areencoded by the designer overhangs as part of prefix and suffixsequences, in certain embodiments a CDS part is defined to extend fromthe second codon of the open reading frame of a gene through the last“sense” codon. For PRO and TER parts extracted from the S. cerevisiaegenome, the disclosure includes boundary definition rules based oncommonly accepted, average sequence length for these two types ofgenetic elements. Specifically, in certain embodiments, yeast PROsegments are defined as the DNA extending 5′ of the ATG codon of thegene of interest for either (i) 500 bp or (ii) the nearest upstream geneboundary, whichever is shorter. TER sequences in certain embodiments aredefined as the sequence 3′ of the CDS that extend either (i) 200 bp or(ii) the nearest downstream gene boundary, whichever is shorter.

Prefix and suffix sequences can be appended to parts in at least threeways: (i) The appropriate overhang can be encoded by primers such thatthe resulting PCR product encodes the appropriate sequences; this istypically done for PRO and TER sequences cloned out of S. cerevisiae.(ii) The prefix and suffix can be built into the design of parts to bemade by polymerase chain assembly or other means of DNA synthesis; thisis typically done for CDSs derived from other organisms as we firstre-code the CDS to optimize codon usage for expression in S. cerevisiaeusing commercially available software (iii) The prefix and suffix couldbe ligated to a pre-existing part as adapter or linker sequences.

In cases where a forbidden site exists internally to a part there aremultiple ways to eliminate the site. Most directly, after subcloning,the forbidden site can be changed using site directed mutagenesis.Alternatively, one can design a modified version of the part to besynthesized. The forbidden type IIS restriction site can be eliminatedby constructing a pair of sub-parts that can be used together in yGGreactions (illustrated in a non-limiting embodiment in FIG. 5). Ingeneral it is considered that changing one base in a PRO or TER part isunlikely to alter the function of the part, and re-coding forbiddensites internal to CDS parts can also be carried out using commerciallyavailable software.

In lieu of changing forbidden sites within part sequences, the yGGreaction conditions can also be modified to skip the five minuteincubation at 50° C., the second to last step. Eliminating the type IISrestriction digest in this step increases the background of intactparental vector, but leaves some proportion of correct assemblies withligated internal sites. Although one would expect both a lower yield ofcorrect assemblies as well a higher background of intact parental vectorto transform E. coli, the detectable selection marker, i.e., thewhite/red selection system built into our yGG workflow makes it easy todistinguish clones with assembled constructs.

Efficiency of yGG Assembly.

The general yGG reaction includes four parts for assembly: a PRO, CDS,TER, and an acceptor vector. In some cases, however, the number of partscan increase, for example if a single CDS is composed of multiplesub-parts or when generating a TU with a C-terminal fusion tag (seebelow). To examine how the number of parts affects assembly efficiencywe compared four- and eight-part yGG reactions using white/red screeningas the output, as described further below. Initially we followed anestablished protocol which specified stock BsaI at 10 U/μL. Here, forthe four-part assembly 92% of recovered colonies were white and for theeight-part assembly 72% of colonies were white (FIG. 3). The observationof red transformants suggested to us that the final yGG reaction productcontained undigested, parental acceptor vector encoding the RFPcassette. We hypothesized that an insufficient active BsaI mightunderlie this result. To test this, we obtained a concentrated stock ofBsaI (100 U/μL) from New England Biolabs to circumvent the problem thataddition of extra BsaI at the standard concentration (10 U/μL) yielded aprohibitive glycerol concentration in the final reaction mixture. Using100 U of BsaI per reaction (1 uL of 100 U/μL), we recovered 95% whitecolonies in the eight-part assembly reaction. Moreover, we discoveredthis result could be re-capitulated for the eight-part assembly (91%white colonies) using only 10 U of the 100 U/μL BsaI stock (0.1 μL).This result indicates that reduced glycerol concentration underlies theimproved BsaI digestion efficiency in yGG reactions. Thus, inembodiments, the disclosure comprises using enzymes having the U/μL andglycerol concentrations described herein.

To test whether white-colored transformants encoded correctly assembledTU constructs, we picked 12 colonies from each reaction condition,prepped the plasmids and digested with an appropriate restriction enzymeto test the assembly structure. For the four-part assembly, in each ofthe three experimental conditions 100% of the selected white coloniesyielded the expected digestion pattern. However, in the eight-partassembly the 10 U, 100 U, and 10 U-low glycerol reactions yielded only7/12, 10/12 and 7/12 correct assemblies, respectively. Four independentincorrect digestion patterns were observed and a single clonerepresenting each class was sequenced to investigate the cause of eachmisassembly. In two cases an internal CDS overhang (TGGT or GTTG)misassembled with a designer overhang in which 2 base pairs weremismatched to a designer overhang (CAGT or TTTT). The third misassemblyoccurred between an internal CDS overhang (ACGG) with 3 base pairmismatches to the designer overhang (CAGT). In the final misassembledclone we analyzed the sequencing reaction failed, possibly due to alarge deletion or a plasmid contamination. Thus, it is considered thatthe overhangs internal to the CDS part assembly should be evaluated on acase by case basis, which can be done by one skilled in the art giventhe benefit of this disclosure.

Based on the foregoing, and without intending to be constrained by anyparticular theory, it is considered that the yGG process (and the VEGASadapter approach described below) may be most efficiently performedusing 10 U of highly concentrated restriction enzyme to minimize theconcentration of glycerol in the reaction. This may be particularlyimportant when assembling TUs with more than four parts. Moreover, ourresults suggest that the faithful assembly of parts in yGG reactionsshould include the use of maximally different overhang sequences whenpossible.

C-Terminally Tagging TUs Generated by yGG.

It is often useful to express a tagged version of a protein forfluorescence microscopy, immunopurification, expression level analysis,etc. To this end we have devised a yGG-compatible strategy to generateTUs encoding C-terminal fusion tags, and thus such TUs, methods ofmaking them and methods of using them are encompassed by thisdisclosure. In these embodiments we assign a special suffix to the CDSpart that permits its assembly into a TU in either the untagged ortagged format. Our design utilizes the enzyme BceAI in combination witheither BsaI or BsmBI (FIG. 4). BceAI is a ‘long reach’ type IISrestriction enzyme that cuts 12 and 14 bp from the recognition leaving a2 base overhang. Although the BceAI recognition sequence is 5 bp inlength, it contains the very rarely encountered CpG dinucleotide and isthus underrepresented in the yeast genome relative to other sequences ofthis length. By embedding a BsaI (or BsmBI) site inside the BceAI site(ACGGCATAGGTCTCGCTCA (SEQ ID NO:3), it is possible to generate one oftwo different overhangs; BsaI (or BsmBI) digestion in a standard yGGreaction generates a standard 3′ CDS overhang of TGAG while BceAIdigestion leaves a 2 base overhang consisting of only the “AC” of thecomplementary strand to the TGA stop codon, allowing read-through tooccur. Due to the moderately unreliable digestion pattern of ‘longreach’ restriction enzymes like BceAI, and to ensure assembly with thedigested fragments, we use annealed oligonucleotides in combination witha standard acceptor vector. Those oligos can contain either a short tag(e.g. flag, V5, HA, etc.), or a linker to ensure the C-terminus of theCDS is in frame with sequences of longer tags (e.g. GFP, mCherry, TAP,GST). Longer tags can be provided as yGG-compatible subcloned constructsto which we assign the 3′ overhang sequence GGAT. In contrast to theuntagged yGG, which may be performed as a ‘one-pot’ reaction, a taggingyGG reaction requires pre-digestion of the CDS construct with BceAI andgel purification prior to the yGG reaction. The disclosure includes eachembodiment described in this approach to tagging TUs.

To test the efficiency of C-terminal tagging by yGG, we built a CDSconstruct with the appropriate sequences flanking HTP1, whose proteinproduct functions in the purine salvage pathway. The HTP1 CDS part wasassembled into a TU by yGG with its native promoter and terminator,along with a V5 tag plus a fluorescent protein tag (either mCherry orGFP). The V5 sequence was provided as annealed oligos and served as alinker to put the fluorescent protein sequence in frame. Assemblyefficiency, assessed by PCR with primers spanning the GFP tag, revealedthat 10 out of 13 white colonies produced amplicons consistent withcorrect assembly. Similar results were obtained with the mCherry tag(data not shown). One of each GFP or mCherry tagged HTP1 TU constructswas then subjected to two functional assays. To determine whether HTP1was expressed we transformed the constructs into a yeast strain in whichADE4 and HTP1 had been deleted from their native genomic loci. In theabsence of HTP1 expression, this strain cannot grow on medium containinghypoxanthine as the sole purine source, however, both the mCherry andGFP tagged HTP1 TUs fully complemented the growth on this medium (FIG.4B). Expression of both mCherry and GFP was also confirmed byfluorescence microscopy (FIG. 4C).

Together this Example demonstrates successful construction ofC-terminally tagged TUs by yGG. The reduced efficiency of assembly hereas compared to the untagged assembly likely lies in the digestion andgel purification step. Specifically, any undigested CDS carried throughthe gel extraction step can lead to untagged TU assembly during the yGGreaction. Additionally, long reach IIS enzymes typically cut with lessprecision than short reach IIS enzymes like BsaI and BsmBI as thesequence composition between the recognition and cut sites can impactDNA movement and stretching.

One of the advantages of the yGG method described herein is the use ofthe bacterial RFP to select against unmodified parental acceptor vector.However, in some cases there is an obvious selection in yeast that candifferentiate between correct and incorrect clones, such as withassembly of an essential yeast transcription unit. In this case, we canbypass the bacterial step and transform the yGG product straight intothe yeast cells, and aspects of this approach are demonstrated inExample 2. A modification that could be made to the yGG acceptor vectorin this case is to express a yeast marker between the BsaI sites.

Although we propose using yGG to assemble yeast transcription units forexpression in yeast, there are other useful applications for this methodand for the VEGAS adapter approach described in Example 2. For example,we have used the PRO and TER sequences to serve as homologous sequencesfor targeted deletion of a specific yeast gene. Using yGG, a selectablemarker gene (URA3, KanMX etc.) can be assembled between the PRO and TERof the gene to be deleted. For this, we built a specific acceptor vector(pAV10) without a yeast selectable marker and lacking a yeastreplication origin. Additionally, we included rare restriction enzyme(NotI and FseI) recognition sites flanking the TU assembly site. Thus,following assembly using yGG, the fragment containing the PRO, markerand TER can be digested and transformed into yeast for targeted deletionof the gene of interest.

yGG can also be used for expression of non-native genes in yeast byassembling a heterologous CDS with a yeast promoter and terminator. Toenable optimal expression in yeast, the gene sequence should be firstcodon optimized for S. cerevisiae, keeping in mind the “forbidden” sitesto ensure efficient assembly.

In addition, the concepts of yGG can easily be adapted to mammalian orplant cells. Expression in mammalian cells may require larger morecomplex promoters but the same yGG concepts can be used once these aredefined. Similarly, there is strong evidence that encoding an intron inmammalian expression constructs has a positive influence on expression.An intron could be contained within the PRO segment, or a separateintron segment could be interposed between the PRO and CDS segments orbetween multiple CDS parts, allowing the evaluation of large numbers ofdifferent introns on gene expression, for example.

Thus, use of the assembly strategy in yGG can be expanded for easycloning in a variety of uses and organisms.

Example 2

This Example provides a significant improvement of the yGG described inthe Example above, but it should be recognized that features of theabove described approach can be included in this Example.

yGG to assemble TUs destined for VEGAS. The yGG method described inExample 1 defines genes as ‘transcription units’ (TUs) comprising threefunctionally distinct types of parts: promoters (PRO; these partssubsume UAS, promoter and 5′ UTR sequences as a single part), codingsequences (CDS), and terminators (TER; consisting of 3′ UTR andpolyadenylation signals). In brief, yGG exploits type IIS restrictionenzymes that cut outside of their recognition sequences exposingdesigner, ‘biologically meaningful’ overhangs to promote assembly offunctional TUs (PRO-CDS-TER) in specially constructed acceptor vectors.A distinction made for TUs destined for VEGAS pathway assembly is theaddition of two additional VEGAS adapter (VA) parts into the assembly.Here, one VA is designed to assemble upstream of the promoter (LVA, forleft VEGAS adapter) and the other for assembly downstream of theterminator (RVA, for right VEGAS adapter). The yGG reaction with VAparts thus generates the following structure: (vectorend)-LVA-PRO-CDS-TER-RVA-(other vector end) (FIG. 6). The RVA and LVAdesigner overhangs and acceptor vector built specifically for assemblingVA-flanked TUs are described below. This aspect of the disclosure canalso be carried out in a ‘one-pot reaction’, is compatible withcombinatorial assembly (i.e. pools of promoters and terminators in asingle reaction), and is amenable to automation.

Designer Overhangs.

Example 1 described yGG overhangs for PRO, CDS, and TER parts (FIG. 6)that are highly compatible with gene expression. To enable the VEGASaspect of this disclosure, we further describe overhang sequences thatenable assembly of a VA upstream of the PRO (LVA) and a second VAdownstream of the TER (RVA). The overhangs for the LVA part areCCTG-LVA-CAGT and the overhangs for the RVA part are TTTT-RVA-AACT. Inone embodiment, a complete structure of a VA-flanked TU assembled by yGGfor VEGAS is as follows: (vectorend)-CCTG-LVA-CAGT-PRO-AATG-CDS-TGAG-TER-TTTT-RVA-AACT (other vectorend) (FIG. 11). For clarity, the bold letters represent the parts.

VEGAS Adapters.

VEGAS adapters are designed to be orthogonal in sequence with respect tothe native S. cerevisiae genome. For compatibility with assembly, eachVA is subcloned into, for example, a kanamycin-resistance vector flankedby, for example, inward-facing BsaI sites; digestion with BsaI exposesoverhangs encoded for yGG-VEGAS assembly. Each VA sequence (Table 3) issubcloned with yGG overhangs for assembly into either the LVA(CCTG-LVA-CAGT) or RVA (TTTT-RVA-AACT) position. As a result, each VAsequence can be assigned for assembly into either the LVA or RVA TUposition in any modified yGG reaction. Our collection of VEGAS adaptersequences (Table 3) currently contains 18 unique VA sequences, each 57bases in length (Table 3). The VA collection can easily be expanded bydesigning new orthogonal sequences by those skilled in the art given thebenefit of the present disclosure. Two considerations for designingadditional VA sequences include: (i) the sequence must not contain BsaIor BsmBI sites (or any other type IIS restriction sites that may be usedfor TU assembly) or sites for enzymes used subsequently to release theassembled TU from the yGG acceptor vector (e.g. FseI or Nod)); (ii) thesequence must be distinct from the S. cerevisiae genome.

yGG Acceptor Vector Designed for Assembling VA-Flanked TUs.

We have constructed acceptor vectors with a custom multiple cloning site(MCS) for assembly of VA-flanked TUs. These vectors derive from pUC19,with all pre-existing instances of BsaI and BsmBI restriction sitesremoved to support the function of the newly installed, custom MCS,which is dependent on the sequential action of these two enzymes. TheMCS encodes a detectable marker, for example, an RFP cassette with an E.coli promoter and terminator sequences that confer a red colony colorupon introduction into E. coli. The RFP cassette is flanked by outwardlyfacing BsaI sites that expose the required VA overhangs for yGG assembly(LVA 5′ end: CCTG; RVA 3′ end: AACT). Successful yGG assembly cuts theRFP cassette out of the plasmid allowing identification of positiveclones by white/red screening. Finally, beyond each BsaI site is encodedan inward facing BsmBI site that can be used to release assembled TUsfor subsequent VEGAS assembly. For assemblies that are incompatible withBsmBI digestion to release the assembled TU (for example if any of theparts encode an internal BsmBI site), we have also built additionalvectors that use NotI or FseI, two rare cutters with 8 bp recognitionsequences, to release assembled TUs flanked by VAs. In principle anyenzyme that does not cut internally to the assembly VA-flanked TU can bebuilt into this acceptor vector, and use of all of such enzymes isencompassed by this disclosure.

VEGAS to Assemble Pathways for Expression in Yeast.

The VAs flanking each assembled TU comprise a condition for implementingVEGAS. Specifically, each VA provides 57 bp of unique sequence that canbe leveraged for homologous recombination-dependent pathway assembly invivo into a specially designed VEGAS acceptor vector (FIG. 7). Thisapproach supports modularity during assembly and re-usability of parts,thereby allowing combinatorial assembly of TUs. We have developed twoillustrative and distinct VEGAS workflows that are described below.Briefly, in the first instance the VAs themselves provide terminalsequence homology for pathway assembly (FIG. 8), while in the secondinstance the VAs serve as primer binding sites for overhang extensionPCR to generate terminal homology (FIG. 9). The latter workflow has asan advantage that the order and orientation of genes in the pathway canbe changed even after TU assembly simply by designing new sets ofprimers. In both cases, a common VEGAS vector is used for pathwayassembly.

VEGAS Vector.

In an embodiment, a VEGAS vector (FIG. 7) is used for pathway assemblyby homologous recombination in S. cerevisiae. It encodes all sequencesrequired for mitotic stability in yeast, including a centromere (CEN),replication origin (autonomously replicating sequence (ARS)), and aselectable marker. A 2 micron origin can also be used in place of theCEN/ARS combination. Because the final assembled construct in yeast iscircular, there is no requirement for telomeres. Further, the vectorencodes a selectable marker and replication origin for propagation in E.coli. Our VEGAS assembly vector design includes a custom multiplecloning site (MCS) in which an E. coli RFP expression cassette isflanked by outward facing BsaI sites; all other instances of BsaI siteshave been recoded or removed from the vector. Digestion with BsaIlinearizes the vector, releasing the RFP cassette and exposingpreviously incorporated terminal VA sequences (VA1 and VA2). MCSs areincluded in this disclosure.

VA Homology VEGAS.

In an embodiment, the order and orientation of all pathway genes isdefined at the outset and VAs are assigned to each TU based on theselected position. Specifically, the LVA assigned to the left-mostpositioned TU encodes a VA sequence ‘1’ (VA1, Table 3) to match one endof the linearized VEGAS assembly vector (see above); adjacent TUs encodeidentical VA sequences assembled in the RVA and LVA positions; finallythe RVA of the right-most TU encodes VA sequence ‘2’ (VA2, Table 3) tomatch the other end of the linearized VEGAS assembly vector (FIG. 7).The TUs of the pathway of interest are assembled in individualreactions, and following E. coli transformation and isolation of acorrectly assembled construct (white colony), the VA-flanked TU insertscan be released by, for example, BsmBI digestion (FIG. 8A). Thedigestion products corresponding to all pathways TUs can then betransformed into yeast along with the linearized VEGAS assembly vectorand the pathway assembled by homologous recombination (FIG. 8B). In thisscenario, gene order and orientation in the assembled pathway are fixedonce the yGG reactions are performed. The position of TUs with respectto one another can only be changed if the TUs are reassembled by yGGwith newly assigned VAs.

PCR-Mediated VEGAS.

In this approach, which is encompassed in the disclosure, a unique VAsequence (Table 3) is assigned to the LVA and RVA positions of each TUin the genetic pathway. As a result, the yGG-assembled VA-flanked TUsencode no terminal sequence homology with one another or with the VEGASassembly vector. Rather, each assembled TU is subjected to PCRamplification using primers that anneal to the VAs and encode specificoverhangs that generate terminal sequence homology between adjacent TUs(and the vector). An advantage to this workflow is the capability tochange the gene order and orientation without having to rebuild each TU,as described above.

Proof-of-Concept: yGG and VEGAS to Assemble the β-Carotene and ViolaceinPathways in S. cerevisiae.

The four gene β-carotene pathway and the five gene violacein pathwayserve as useful tools to develop DNA assembly strategies as pathwayexpression can be tracked by the development of colored yeast.Expression of violacein pathway genes (vioA, vioB, vioC, vioD, and vioEfrom Chromobacterium violaceum can turn yeast purple, while expressinggenes of the β-carotene pathway (crtE, crtI, crtYB fromXanthophyllomyces dendrohous) yields orange colonies. Color productionin both cases is quantitatively and qualitatively dependent on pathwayflux and thus on the expression levels of pathway genes. For instance,overexpression of the catalytic domain of the S. cerevisiae HMG CoAreductase HMG1 (tHMG1) can dramatically alter carotenoid production,yielding yellow colonies. As proof-of-concept of the VEGAS methodologywe have assembled carotenoid and violacein pathways for expression in S.cerevisiae using yGG-assembled VA-flanked TUs.

VA Homology.

To demonstrate VEGAS using terminal homology encoded in the VAsequences, we assigned each β-carotene pathway CDS a unique S.cerevisiae promoter and terminator (Table 4) and pre-determined thedesired, left-to-right assembly order (FIG. 10A). A strong promoter wasassigned to each CDS for high expression of each gene. In the VEGASexperiments presented here we included the KanMX TU (pre-assembled as aPRO-CDS-TER yGG part), whose protein product yields resistance to thedrug G418, to permit a secondary plate-based screening approach using anunselected marker to test for efficiency of correct assemblies in yeast.Based on the pre-defined gene assembly order (FIG. 10A) we assigned theappropriate LVA and RVA to each TU. Subsequent to yGG, a correctlyassembled TU (white colony) for each of the five reactions was selectedand the pathway assembled by VEGAS via co-transformation ofBsmBI-digested TUs plus the linearized VEGAS assembly vector. Theprimary selection for assembly was carried out on medium lacking uracil(SC-Ura), as the URA3 gene was encoded on the assembly vector (FIG. 5A).Almost all colonies growing on the SC-Ura plate were yellow in color,consistent with assembly of a functional pathway that includes tHMG1(13) (FIG. 10B, left panel). Moreover, following replica plating ontoYPD medium supplemented with G418, virtually 100% of colonies were G418resistant as expected for 100% correct assembly (FIG. 10B, right panel).The variation in color (light yellow versus darker yellow or evenorange) between colonies may result from stochasticity in expression ofpathway genes between colonies, mis-assembly (for instance absence oftHMG1 TU, see below), or variation in plasmid copy number (e.g. twocopies versus one); indeed the yellow colony color typically normalizesacross the plate with incubation for several more days.

PCR-Mediated Homology.

In this approach, which is encompassed in this disclosure, unique VAsequences were assigned to the LVA and RVA position for each of the 4β-carotene pathway TUs plus the KanMX TU (Table 5). The promoter andterminator parts for each CDS as well as the defined left-to-right geneorder were not changed as compared to the adapter homology experimentdescribed previously (Table 4 compared to Table 5). Following yGGassembly, the reaction mixtures were used directly for five independentPCRs to amplify each TU with primers encoding ˜20 nucleotides (nt) ofsequence to anneal to the VA plus ˜30 nt of assigned neighboringhomology sequence; together this yielded ˜50 bp of terminal homologybetween adjacent parts for VEGAS (FIG. 11A). The PCR products wereco-transformed along with the linearized VEGAS assembly vector intoyeast and selection for assembly was carried out on SC-Ura medium. Here˜95% of colonies developed a yellow color on SC-Ura and virtually 100%of colonies were also G418 resistant (FIG. 11B). Compared to theadapter-mediated homology assembly (FIG. 10B), more colonies appearedwhite in color (˜5% compared to ˜1% in FIG. 10B) and most of these werealso G418 resistant, suggesting a slightly lower fidelity of assembly inthis approach. When a single yellow-colored, Ura⁺, G418^(r) colony wasrestreaked on YPD medium supplemented with G418, all resulting colonieswere of a uniform yellow color (FIG. 11C, left panel). The assembledpathway from this colony was recovered into E. coli and the plasmidstructure confirmed by digestion and sequencing (data not shown).

To demonstrate versatility of the PCR-mediated VEGAS approach, weassembled a different version of the β-carotene pathway, this timeomitting the tHMG1 TU. To accomplish this, we re-used the previously yGGassembled, VA-flanked TUs for crtE, crtI, KanMX marker, and crtYB, andsimply amplified the crtYB TU with a different primer encoding terminalhomology to the VEGAS (FIG. 11C, right panel). Transformation platesresembled those shown in FIG. 11B but the assembly yielded coloniesproducing an orange color (FIG. 11C, right panel). The structure ofassemblies producing orange yeast cells was validated by recovery intoE. coli and digestion (data not shown).

In another embodiment, we constructed the violacein pathway usingPCR-mediated VEGAS of the five violacein TUs plus the KanMX cassette;together this was a seven-piece assembly including the vector backbone.TUs were assembled with flanking VAs by yGG (Table 6), and terminalhomology between adjacent parts was introduced by PCR. Transformationinto yeast of all parts required for pathway assembly, as compared to acontrol experiment omitting the KanMX part, yielded a substantialincrease in the number of colonies producing a purple pigment on theprimary SC-Ura transformation plates (FIG. 11D). This color developed inall colonies upon re-streaking (FIG. 11D). White colonies may arise frommis-assemblies or from circularization of the parental, empty VEGASvector. The structure of assemblies producing purple yeast colonies wasvalidated by recovery into E. coli and digestion, and was found to becorrect in 7/7 independent colonies (data not shown).

yGG and VEGAS for Combinatorial Pathway Assembly

An advantage of VEGAS is its compatibility with combinatorial assembly,made possible by the modularity provided by the VA sequences. Todemonstrate this, we generated combinatorial transcription unit (TU)libraries for each of the four β-carotene pathway genes and then usedPCR-mediated VEGAS to assemble the TU libraries into combinatorialpathways for expression in yeast. With a pool of 10 promoters and 5terminators in each TU combinatorial assembly (Table 7), the theoreticallibrary complexity exceeded 60,000 possible combinations. For thisexperiment the 5 TUs were assigned the same VAs as in Table 5, so thesame primers were used to generate amplicons with terminal homology.Following VEGAS in S. cerevisiae, we observed a wide diversity of colonycolors on the transformation/G418 replica plate (FIG. 12A). Weinterrogated the stability and robustness of expression of the assembledpathways by re-streaking transformants representing many differentcolors for single colonies (FIGS. 12B and C.) Sequence analysis of fiveconstructs conferring uniquely colored yeast colonies (orange, brightyellow, light pink, light yellow, white) revealed the presence of all 10promoters and 4 of the 5 terminators in at least one position in anassembled pathway, consistent with unbiased combinatorial assemblyreactions (FIG. 12E-H). Finally, we assessed the production of threecarotenoid compounds in yeast cells expressing four unique β-carotenepathways (strains from FIG. 12D-G). Indeed, we observed differentabundances of β-carotene, phytoene, and lycopene in these strains (FIG.12I). While each of the yellow and orange strains produce two to threetimes more β-carotene than the pink colored strain, it is likely theabundance of lycopene that differentiates the orange from the yellowstrain. On the other hand both yellow strains produce an abundance ofphytoene, an early intermediate in the β-carotene pathway, suggestingflux could still be improved by additional pathway engineering;alternatively, additional transformants could be screened to identifyassembled pathways that yield higher β-carotene titres.

Biosynthetic pathways typically consist of multiple genes whoseindividual protein products function much like an assembly line,converting an initial substrate, through some number of intermediatesteps, into a desired end product. Expressing biosynthetic pathways inS. cerevisiae, in particular those not natively encoded in the S.cerevisiae genome, is desirable as it effectively converts thismicroorganism into a cellular factory capable of producing valuablecompounds. A major consideration is tuning expression of individualgenes to optimize flux through the pathway, given that balanced geneexpression can often trump simple overexpression of each pathway genewith respect to yield. High-level constitutive expression may create asignificant metabolic burden on the cell, or lead to the accumulation oftoxic foreign intermediates. For example, violacein is toxic to yeastcells at high concentration (22), which may contribute to the slowergrowth of purple colonies as compared to white ones on the VEGASviolacein assembly plates (FIG. 11D).

It will be apparent from the foregoing that in the present disclosure weaddress the challenge of assembling and tuning genetic pathways withVEGAS, a modular approach that allows facile assembly of TUs flanked byVEGAS adapters (VAs) into complete genetic pathways by homologousrecombination in yeast. Gene expression can be controlled by assigningdesired regulatory elements (PRO and TER parts) up front or, as wedemonstrate for the β-carotene pathway, in a combinatorial manner. Manyprevious studies investigating the expression of β-carotene expressionin S. cerevisiae have relied on a previously built construct encodingcrtE, crtI, and crtYB, each expressed using an identical promoter andterminator combination. Here, using VEGAS/yGG we construct andcharacterize six new β-carotene pathway expression cassettes; inprinciple we could characterize any number of additional constructsassembled using the combinatorial approach. These constructs representuseful new resources since they display a high degree of geneticstability in yeast, evidenced by the uniformity of colony color (FIGS.11 and 12). Presumably the observed genetic stability is a function ofthe use of unique promoters and terminators flanking each CDS. Notably,the constructs derived from the combinatorial assembly share at leastone common part (FIG. 12D-H); based on this disclosure, in futurecombinatorial assembly experiments, this could easily be overcome byincreasing the number of PRO and TER parts used during combinatorialassembly.

VEGAS specifies episomal expression of the assembled genetic pathway,which comes with certain qualities. Episomal expression allows one toleverage a variety of systematic screening tools available for S.cerevisiae, for instance the deletion mutant collection or theoverexpression array, since the pathway can easily be moved betweenstrains. Moreover, state-of-the art approaches such as SCRaMbLE) ofsynthetic chromosomes (constructed as part of the Sc2.0 Synthetic YeastGenome Project (www.syntheticyeast.org), can be implemented to identifyfavorable genetic backgrounds for pathway expression. However, the useof selective medium or the addition of a drug to ensure maintenance ofthe pathway construct may lead to decreased product yield. One solutionis to make the plasmid essential in the strain background such that itcannot be lost; this approach could be implemented either as part of theVEGAS workflow, or at a later date once the desired construct isintroduced into the most favorable strain background. Of course, a VEGASassembly vector could also be constructed (or retrofitted) such thatfollowing episomal VEGAS pathway assembly and characterization thepathway could be integrated into the genome, given the benefit of thisdisclosure.

The use of computationally derived orthogonal sequences provides apowerful tool for DNA assembly, as described here using yeast andelsewhere using in vitro methods. S. cerevisiae, with its inherentcapacity for homologous recombination, is a useful cloning tool; thestandardized and modular assembly of genetic pathways by yGG/VEGAS neednot be limited to expression in S. cerevisiae. Rather, pathwaysassembled episomally in yeast using this approach can easily betransferred to other microorganisms, in particular those that are notproficient at homologous recombination.

Example 3

The following materials and methods were used to obtain the resultsdescribed above. One-pot yGG Assembly. TU parts (PRO, CDS and TER), eachsubclone cloned into a Kanamycin resistant vector (pCR Blunt II TOPO,Invitrogen/Life technologies, Carlsbad, Calif. 450245), were combined inequimolar amounts and mixed with Reaction Master Mix [1.5 μl 10×T4 DNAligase reaction buffer (New England Biolabs, M0202), 0.15 μl 100× BovineSerum Albumin (BSA, New England Biolabs), 600 U T4 DNA ligase (rapid)(Enzymatics, Beverly, Mass., L6030-HC-L) and 10 U or 100 U of BsaIor/and BsmBI (New England Biolabs, Beverly, Mass., R0535 or R0580,respectively)] to a final volume of 15 μL. The high concentration BsaIwas a custom order from New England Biolabs. One-pot digestion-ligationassembly was performed in a thermo-cycler as follows: 25 cycles of 37°C. for 3 min and 16° C. for 4 min, followed by 50° C. for 5 min and 80°C. for 5 min. 5 μL of each assembly reaction was transformed into 50 μLof competent DH5a E. coli cells and plated on the appropriate selectionmedia. For C-terminal tagging yGG assembly reactions, before the one-potyGG assembly, 1 μg of cloned CDS was digested with BceAI, loaded on agel and the appropriate band was extracted (Zymo Research, Irvine,Calif.).

Design of VEGAS Adapter Sequences.

From a previously generated, in-house collection of 10mer sequences thatrarely occur in the S. cerevisiae genome, 60mers were randomly producedby concatenation in silico. The eighteen 60mers with the lowestsimilarity to the S. cerevisiae genome were selected to comprise theinitial set of VA sequences reported here. For cost minimization, the VAsequences were subsequently shortened to 57mers by deleting threeterminal base pairs (Table 3). Alternatively, the web-based tool R2oDNAcan be used to design orthogonal sequences for use as VA sequences,given the benefit of the present disclosure.

Vector Construction.

To construct the yGG acceptor vector for TUs destined for VEGAS, pUC19)was modified using a known approach. Briefly, all pre-existing instancesof BsaI and BsmBI sites were re-coded or deleted and a custom multiplecloning site was installed, encoding an E. coli RFP expression cassetteflanked by outward-facing BsaI sites designed to leave 5′ and 3′ VAdesigner overhangs (top strand: CCTG and AACT, respectively).Additionally, neighboring Nod and FseI sites, or inward-facing BsmBIsites were further encoded outside of the BsaI sites to facilitateexcision of assembled VA-flanked TUs from the construct. Plasmididentification numbers are: pNA0178 (NotI and FseI) and pJC120 (BsmBI).To construct the VEGAS assembly vector, a previously constructed yGGacceptor vector (11), pAV116, which derives from pRS416 (12), was used.VA1 and VA2 sequences, plus BsaI sites (as shown in FIG. 7) were thenintroduced up and downstream of an E. coli RFP expression cassette.

Parts Cloning.

The β-carotene CDS parts crtE, crtI, and crtYB, were amplified fromgenomic DNA of an S. cerevisiae strain previously engineered to expressthe pathway (13). Codon optimized violacein biosynthetic enzyme CDSparts, vioA, vioB, vioC, vioD, and vioE, were synthesized. The truncatedversion of HMG1 (tHMG1) plus all PRO and TER parts were amplified fromgenomic DNA extracted from the BY4741 strain of S. cerevisiae. Primersused for amplification included overhangs encoding inward-facing BsaIsites separated by one base from the appropriate yGG-compatibleoverhangs. All parts were subcloned using the Zero Blunt TOPO PCRcloning kit (Life Technologies; 45-0245), transformed into E. coli(Top10 cells), and sequence verified. CDS parts that encoded BsaI orBsmBI sites were re-coded by Multichange Isothermal mutagenesis (MISO)using an established approach. All parts and their correspondingsequence files are available upon request.

Yeast Golden Gate (yGG) into the VEGAS yGG Acceptor Vector.

100 ng of yGG acceptor vector (pJC120 for all experiments described inthis work) plus equimolar amounts of each part for assembly (LVA, PRO,CDS, TER, RVA) were combined in a Golden Gate reaction consisting of:1.5 μL 10×T4 DNA ligase reaction buffer (New England Biolabs, M0202),0.15 μL 100× Bovine Serum Albumin (BSA, New England Biolabs), 600 U T4DNA ligase (rapid) (Enzymatics, L6030-HC-L) and 10 U of BsaI (NewEngland Biolabs, R0535) in a final volume of 15 μL. One-potdigestion-ligation assembly was carried out in a thermocycler byperforming 25 cycles of [37° C. 3 min, 16° C. 4 min], followed by 50° C.5 min, and 80° C. 5 min. We have also described above severalmodifications to improve the efficiency of yGG. For ‘terminal homologyVEGAS’ experiments, 5 μL of each yGG reaction was transformed into Top10E. coli and plated on LB plates supplemented with carbenicilllin (75μg/ml). White colonies were selected for verification of assemblyconstructs by restriction digest. For combinatorial assembly, PRO or TERparts were mixed in equal molar amounts prior to yGG assembly.

Terminal Homology VEGAS.

˜1 μg of yGG-assembled, VA-flanked TU constructs were digested withBsmBI (New England Biolabs, R0580) in a final volume of 20 μL. 2 μL(˜100 ng) of each digestion product was used directly for yeasttransformation along with ˜50 ng of BsaI-linearized VEGAS assemblyvector (pJC170 for all experiments described in this work). Yeasttransformations were carried out using established approaches exceptcells were heat shocked for only 15 minutes in the presence of 10% DMSOat 37° C. and prior to plating were incubated in 400 μL of 5 mM CaCl₂for 10 minutes at room temperature. For all VEGAS yeast transformations,following primary selection on SC-Ura plates (incubated 3 days at 30°C.), plate images were taken and transformation plates were replicaplated onto YPD medium supplemented with G418 (200 μg/mL). A second setof plate images was taken three days post-replica plating.

PCR-Mediated VEGAS.

Primers were designed to anneal to the leftmost and rightmost ends ofthe LVA and RVA sequences, respectively. Each primer additionallyencoded 30 bp of overhang sequence homologous to the adjacent VAsequence. 1 μL of each yGG reaction was used directly in a PCR reactionwith Phusion High-Fidelity DNA Polymerase (M0530L) to amplify theVA-flanked TU and incorporate neighboring homology. 5 μL of each PCRreaction was transformed directly into yeast along with ˜50 ng ofBsaI-linearized VEGAS assembly vector (pJC170 for all experimentsdescribed in this work). Yeast transformation and replica plating stepswere performed as described in the “Terminal Homology VEGAS” section.

Plasmid Recovery from Yeast.

Following VEGAS, assembled constructs encoding the β-carotene andviolacein pathways were recovered from yeast using an establishedapproach except that in all cases constructs were recovered from 3 mL ofcultured yeast (SC-Ura), inoculated from a single yeast colony, and theblue-white E. coli screening step following transformation was omitted.For combinatorial assembly of the β-carotene pathway, PRO and TER partsflanking each CDS were determined by Sanger sequencing of the recoveredplasmid.

Carotenoid Production.

Four constructs encoding β-carotene pathways (pJC175, orange; pJC178,bright yellow; pJC181, pink; pJC184, light yellow), each a product ofcombinatorial PCR-mediated VEGAS (FIG. 9E-H), were used. Threeindependent colonies of each were inoculated into 10 mL of YPD mediumsupplemented with G418 (200 μg/mL) and grown to saturation (3 days at30° C., 250 rpm). Carotenoids were extracted using a PRECELLYS® 24high-throughput tissue homogenizer. Briefly, 1 mL of culture waspelleted in a PRECELLYS tube and the pellet was extracted with 1 mLtetrahydrofuran (containing 0.01% butylhydroxytoluene (BHT)) byhomogenization for 3×15 seconds at 6500 rpm. Following centrifugationfor five minutes at 4° C., 800 μL was then transferred to a glass vial.Extracts were dried down and resuspended in 80 μL dichloromethanefollowed by 720 μL of a 50:50 (v/v) mixture of heptane and ethyl acetate(containing 0.01% BHT). HPLC analysis of carotenoids was performed usingstandard techniques.

TABLE 1 Standardized prefix and suffix sequences for yGG. BsaI BsaIBsmBI BsmBI prefixes suffixes prefixes suffixes PRO GGTCTCA AATGCGACGTCTCA AATGCGA CAGT GACC CAGT GACG (SEQ ID (SEQ ID (SEQ ID (SEQ IDNO: 4) NO: 5) NO: 6) NO: 7) CDS GGTCTCA TGAGCGA CGTCTCA TGAGCGA AATGGACC AATG GACG (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 8) NO: 9) NO: 10)NO: 11) TER GGTCTCA TTTTCGA CGTCTCA TTTTCGA TGAG GACC TGAG GACG (SEQ ID(SEQ ID (SEQ ID (SEQ ID NO: 12) NO: 13) NO: 14) NO: 15) Bold face 6 bpsequences are recognition sites; Italicized 4 base sequences areoverhang sites. All sequences are written 5′ to 3′ on the “top strand”of the final part.

TABLE 2 Acceptor vectors Yeast Yeast Yeast marker replicationintegrative E. coli Plasmid Addgene Plasmid name (organism) parts locusmarker 2°RE_(b) number ID CEN/ARS (low copy) pAV113 HIS3 (Sc) CEN/ARSn/a Amp n/a pLM108 63180 pAV114 TRP1 (Sc) CEN/ARS n/a Amp n/a pLM26463181 pAV115 LEU2 (Sc) CEN/ARS n/a Amp n/a pLM109 63182 pAV116 URA3 (Sc)CEN/ARS n/a Amp n/a pLM304 63183 pAV11K KanMX CEN/ARS n/a Amp n/a pLM20063184 pAV113.loxP_(a) HIS3 (Sc) CEN/ARS n/a Amp n/a pJC081 63186pAV115.loxP_(a) LEU2 (Sc) CEN/ARS n/a Amp n/a pJC082 63187pAV116.loxP_(a) URA3 (Sc) CEN/ARS n/a Amp n/a pJC106 63188 2 micron (μ)(high copy) pAV123 HIS3 (Sc) 2μ n/a Amp n/a pAM090 63189 pAV124 TRP1(Sc) 2μ n/a Amp n/a pLM266 63190 pAV125 LEU2 (Sc) 2μ n/a Amp n/a pLM27063191 pAV126 URA3 (Sc) 2μ n/a Amp n/a pAM078 63192 Integrative pAV103HIS3 (Sc) n/a HIS3 Amp n/a pLM346 63193 pAV104 TRP1 (Sc) n/a TRP1 Ampn/a pLM262 63194 pAV105 LEU2 (Sc) n/a LEU2 Amp n/a pLM107 63195 pAV106URA3 (Sc) n/a URA3 Amp n/a pLM302 63196 pAV10.F3 HIS3 (Sc) n/a chrVI:Cam NotI pSIB055 63199 97873-98803 or BciVI pAV10.F3.loxP_(a) HIS5 (Sp)n/a chrVI: Amp NotI pSIB581 63200 97873-98803 pAV10.F6.loxP_(a) URA3(Kl) n/a chrVI: Amp NotI pSIB582 63201 97873-98803 or BciVIpAV10.K3.loxP_(a) HIS5 (Sp) n/a YKL162C-A Amp NotI pSIB584 63202pAV10.K6.loxP_(a) URA3 (Kl) n/a YKL162C-A Amp NotI pSIB585 63203 orBciVI pAV10.K5.loxP_(a) LEU2 (Sc) n/a YKL162C-A Amp NotI pSIB586 63204or BciVI pAV10.HO3.loxP_(a) HIS5 (Sp) n/a HO locus Amp NotI pSIB58763205 pAV10.HO5.loxP_(a) LEU2 (Sc) n/a HO locus Amp NotI pSIB589 63206or BciVI pAV10.K3 HIS5 (Sp) n/a YKL162C-A Amp NotI pSIB596 63207pAV10.KH hygromycin n/a YKL162C-A Amp NotI pSIB599 63208 pAV10.KN cloNATn/a YKL162C-A Amp NotI pSIB601 63209 pAV10.K5 LEU2 (Sc) n/a YKL162C-AAmp NotI pSIB604 63210 or BciVI pAV10.HO6 URA3 (Kl) n/a HO locus AmpNotI pSIB843 63211 or BciVI pAV10.K4 TRP1 (Sc) n/a chrIXR: Amp n/apKF091 63212 387328-388330 pAV10 n/a n/a n/a Amp NotI pNA0179 63213 orFseI _(a)“.loxp’ indicates the inclusion of loxp sites in the yGGvector. The TU is flanked by two Loxp sites. _(b)“2°RE” refers to thesecondary restriction enzyme used to release an assembled TU prior tointegrative yeast transformation. Sc, Saccharomyces cerevisiae; Sp,Schizosaccharomyces pombe; Kl, Kluyveromyces lactis; Amp, ampicillin;Cam, chloramphenicol. For additional information on yGG acceptor vectornomenclature see FIG. 2.

TABLE 3 VEGAS adapter sequences Name Sequence (5′-3′) VA1*CCCCTTAGGTTGCAAATGCTCCGTCGACGGGATCTGTCCTTCTCTGCCGGCGATCGT (SEQ ID NO: 1) VA2**TGACGCTTGGATGCGTGACCCCGTACGTCATGACCCGTCATGGGTATGTAAGCGAAG (SEQ ID NO: 2) VA3GGAGGTACTGGCCTAGCGTCGTGGCCCGGGAGAGACAGTTTAGTAGTGACTCGCGGC (SEQ ID NO: 16) VA4TTGGCGTTAATTGTAGCTTATTTCCCGCCCTGTGATTGAGGCGGGATGGTGTCCCCA (SEQ ID NO: 17) VA5GACTAAGACTCTGGTCACGGTTCAGAAGTGGACGATGCATGTCGTCGGGCTGATAGA (SEQ ID NO: 18) VA6TGCACGGCGCTAGGTGTGATATCGTACACTTGGGAGAAGTCAGATACGATTGCGGCT (SEQ ID NO: 19) VA7TAGCGGCGCCGGGAAATCCAGCATATTCTCGCGGCCCTGAGCAGTAGGTGTCTCGGG (SEQ ID NO: 20) VA8GAGTCTACGTTACACCTGAACTCGCATGTCTGGGGTTGTGGTCAGGCCTTGTCAATT (SEQ ID NO: 21) VA9GCGTACTGGCCGCCCGGGCCTGATGTGGCCGTCCTATTAGCATTGTACACCCTCATT (SEQ ID NO: 22) VA10CTTGAATCGGCTTTAGGATCCGGTACTGCCGACGCACTTTAGAACGGCCACCGTCCT (SEQ ID NO: 23) VA11GCAAGTTTTGAAGAGGTGTAAACTCTCCGCAGCACCTCCGGACTATGCCCGAGTGGT (SEQ ID NO: 24) VA12TGAAGCTACGCGCCGAGCGTCTGACTCCTTTAGTCCGCGTCATCGCTTTGAGCGCGT (SEQ ID NO: 25) VA13TCCGGATCCCTTTCGGTCCATATAGCGGATTTCCATAGACGTAGACCGCGCCAATGT (SEQ ID NO: 26) VA14GACGACGCGTTCTGTGTCTTCGTTGCGGCTCTGCGCTTGGTCGTTGGCGACGGCCGT (SEQ ID NO: 27) VA15TGTAAGGGCGTCTGTTAACCCAAGGTCCCTCGAACCGTATGCAGAGCCGTGGCTACG (SEQ ID NO: 28) VA16TATCGCGGGTGCGTGCATCGACAAGCCATGCCCACCTTCTGGTCGATTGGGCTGGCG (SEQ ID NO: 29) VA17CATCCATCGATATTTGGCACTGGACCTCAACGCTAGTGTTCGCGGACTGCACTACCT (SEQ ID NO: 30) VA18GATTAAGGGGCATACCGTGCCTATCCTGGTAATTGTGTAGGCTACCTGTCTGTATAC (SEQ ID NO: 31) *encoded terminally on the left armof the linearized VEGAS assembly vector **encoded terminally on theright arm of the linearized VEGAS assembly vector

TABLE 4 yGG parts for adapter homology-mediated assembly of the β-carotene pathway by VEGAS TU order (left to right) LVA PRO CDS TER RVA 1VA1 pTDH3 crtE ttACS2 VA3 2 VA3 pPGK1 crtI ttENO2 VA4 3 VA4 — KanMX TU —VA5 4 VA5 pACT1 crtYB ttASC1 VA6 5 VA6 pRPS2 tHMG1 ttCIT1 VA2

TABLE 5 yGG parts for PCR-mediated assembly of the β-carotene pathway byVEGAS TU order (left to right) LVA PRO CDS TER RVA 1 VA7 pTDH3 crtEttACS2 VA3 2 VA8 pPGK1 CrtI ttENO2 VA4 3 VA9 — KanMX TU — VA5 4 VA10pACT1 crtYB ttASC1 VA6 5 VA11 pRPS2 tHMG1 ttCIT1 VA12

TABLE 6 yGG parts for PCR-mediated assembly of the violacein pathway byVEGAS TU order (left to right) LVA PRO CDS TER RVA 1 VA7 pTDH3 vioAttACS2 VA3 2 VA8 pPGK1 vioB ttENO2 VA4 3 VA9 — KanMX TU — VA5 4 VA10pACT1 vioC ttASC1 V6 5 VA11 pRPS2 vioD ttCIT1 VA12 6 VA16 pZEO1 vioEttFUM1 VA5

TABLE 7 Promoter and terminators pools for combinatorial assembly PROTER pTDH3 ttACS2 pPGK1 ttENO2 pACT1 ttASC1 pRPS2 ttCIT1 pZEO1 ttSIK1pIRR1 pALG7 pSWE1 pTIP1 pHSL1

These following parts were used to examine yGG efficiency. BsaI sitesare marked in red, overhangs are marked in blue. In both 4 part and 8part assemblies pAV113 (Table 2) was used as an acceptor vector and theGAL1 promoter and terminator were used with the appropriate overhangs:

>GAL1p (SEQ ID NO: 31) ggtctcacagtTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGATAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAaatgcgagacc >GAL1t (SEQ ID NO: 32)ggtctcatgagGTATACTTCTTTTTTTTACTTTGTTCAGAACAACTTCTCATTTTTTTCTACTCATAACTTTAGCATCACAAAATACGCAATAATAACGAGTAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGATACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGTTCTTGGCAAGTTGCCAACTGACGAGATGCAGTAAAAAGAGATTGCCGTCTTGAAACTTTTTGTCCTTTTTTTTTTCCGGGGACTCTACGAGAACCCTTTGTCCTACTGATTAATTTTGTACTGAATTTGGACAATTCAGATTTTAGTAGACAAGCGCGAGGAGGAAAAGAAATGACAGAAAAATTCCGATGGACAAGAAGATAGGAAAAAAAAAAAGCTTTCACCGATTTCCTAGACCGGAAAAAAGTCGTATGACATCAGAATGAAAAATTTTCAAGTTAGACAAGGACAAAATCAGGACAAATTGTAAAGATATAATAAACTATTTGATTCAGCGCCAATTTGCCCTTTTCCATTTTCCATTAAATCTCTGTTCTCTCTTACTTATATGATGATTAGGTATCATCTGTATAAAACTCCTTTCTTAATTTCACTCTAAAGCATACCCCATAGAGAAGATCTTTCGGTTCGAAGACATTCCTACGCATAATAAGAATAGGAGGGAATAAttttcgagacc

For the 4 part assembly we used ADE13 CDS with the appropriateoverhangs:

>ADE13_CDS (SEQ ID NO: 33)ggtctcaaATGCCTGACTATGACAATTACACTACGCCATTGTCTTCTAGATATGCCTCCAAGGAAATGTCAGCAACGTTTTCTTTGAGAAACAGATTTTCCACATGGAGAAAACTATGGTTAAATTTGGCTATTGCTGAGAAGGAATTGGGCTTAACTGTTGTTACAGATGAAGCAATTGAGCAAATGCGCAAACACGTCGAAATCACTGATGATGAAATCGCAAAAGCTTCTGCTCAAGAAGCCATTGTAAGACATGATGTTATGGCACATGTTCATACATTTGGTGAAACTTGTCCGGCTGCTGCGGGTATCATTCACTTAGGTGCTACTTCCTGTTTCGTTACAGACAATGCTGATCTAATCTTTATTAGGGACGCCTACGATATTATTATTCCAAAACTTGTTAACGTCATCAACAGATTGGCTAAGTTTGCTATGGAATACAAGGATTTGCCTGTATTGGGTTGGACTCACTTTCAACCAGCACAATTAACGACCTTGGGTAAGAGAGCTACTTTATGGATACAAGAGCTATTGTGGGATTTGAGAAACTTTGAAAGAGCTAGAAACGATATCGGTCTACGTGGTGTTAAGGGTACTACTGGTACTCAGGCATCATTCTTGGCCTTATTCCATGGTAATCATGATAAAGTTGAAGCCCTTGACGAAAGAGTAACTGAATTATTAGGTTTCGATAAGGTATATCCAGTCACTGGTCAAACCTACTCAAGAAAAATTGACATTGACGTGTTGGCTCCTTTGTCTTCTTTTGCTGCTACTGCACACAAAATGGCTACTGACATAAGATTATTAGCCAACCTGAAGGAAGTTGAGGAACCTTTTGAGAAATCACAAATCGGATCCTCTGCTATGGCTTACAAGAGAAACCCAATGCGTTGTGAGAGAGTGTGCTCCTTGGCTAGACACTTAGGTTCCTTGTTTAGTGACGCCGTTCAAACTGCATCCGTTCAATGGTTCGAAAGAACTCTGGATGATTCTGCTATTAGAAGAATTTCTTTACCAAGTGCATTTTTAACCGCAGATATTCTATTATCTACTTTGTTGAACATCTCATCCGGTTTAGTTGTGTATCCAAAGGTTATCGAAAGGAGAATTAAGGGTGAACTACCTTTTATGGCTACTGAAAATATCATCATGGCTATGGTAGAAAAGAATGCCTCCAGACAAGAAGTACATGAGCGTATTAGAGTGCTCTCTCATCAAGCCGCAGCAGTAGTCAAGGAAGAAGGTGGGGAAAATGATTTAATTGAACGAGTAAAGAGGGATGAATTTTTCAAGCCTATCTGGGAAGAATTAGATTCTTTACTGGAACCATCCACTTTTGTTGGTAGAGCTCCACAACAAGTTGAGAAATTTGTTCAAAAAGACGTTAACAATGCTTTACAACCTTTCCAAAAGTACCTAAACGATGAACAAGTCAAGTTAAATGTTtgagcgagacctatgccgt

For the 8 part assembly we used the FAS2 CDS that was cut into 5 partswith the appropriate overhangs:

>FAS2_CDS_Part1 (SEQ ID NO: 34)ggtctcaaATGAAGCCGGAAGTTGAGCAAGAATTAGCTCATATTTTGCTAACTGAATTGTTAGCTTATCAATTTGCCTCTCCTGTGAGATGGATTGAAACTCAAGATGTTTTTTTGAAGGATTTTAACACTGAAAGGGTTGTTGAAATCGGTCCTTCTCCAACTTTGGCTGGGATGGCTCAAAGAACCTTGAAGAATAAATACGAATCTTACGATGCTGCTCTGTCTTTACATAGAGAAATCTTATGCTATTCGAAGGATGCCAAAGAGATTTATTATACCCCAGATCCATCCGAACTAGCTGCAAAGGAAGAGCCCGCTAAGGAAGAAGCTCCTGCTCCAACTCCAGCTGCTAGTGCTCCTGCTCCTGCAGCAGCAGCCCCAGCTCCCGTCGCGGCAGCAGCCCCAGCTGCAGCAGCTGCTGAGATTGCCGATGAACCTGTCAAGGCTTCCCTATTGTTGCACGTTTTGGTTGCTCACAAGTTGAAGAAGTCGTTAGATTCCATTCCAATGTCCAAGACAATCAAAGACTTGGTCGGTGGTAAATCTACAGTCCAAAATGAAATTTTGGGTGATTTAGGTAAAGAATTTGGTACTACTCCTGAAAAACCAGAAGAAACTCCATTAGAAGAATTGGCAGAAACTTTCCAAGATACCTTCTCTGGAGCATTGGGTAAGCAATCTTCCTCGTTATTATCAAGATTAATCTCATCTAAGATGCCTGGTGGGTTTACTATTACTGTCGCTAGAAAATACTTACAAACTCGCTGGGGACTACCATCTGGTAGACAAGATGGTGTCCTTTTGGTAGCTTTATCTAACGAGCCTGCTGCTCGTCTAGGTTCTGAAGCTGATGCCAAGGCTTTCTTGGACTCCATGGCTCAAAAATACGCTTCCATTGTTGGTGTTGACTTATCATCAGCTGCTAGCGCTAGTGGTGCTGCCGGTGCAGGTGCTGCTGCCGGTGCAGCTATGATCGATGCTGGCGCTCTGGAAGAAATAACCAAAGACCACAAGGTTTTGGCGCGTCAACAACTGCAAGTATTGGCTCGTTATCTAAAAATGGACTTGGATAACGGTGAAAGAAAGTTCTTGAAAGAAAAGGACACTGTTGCTGAACTTCAAGCTCAGTTGGATTACTTGAATGCCGAATTAGGTGAATTCtgagacc >FAS2_CDS_Part2 (SEQ ID NO: 35)ggtctcaATTCTTTGTTAACGGTGTTGCTACTTCTTTCTCTAGAAAAAAGGCCAGAACCTTCGATTCTTCCTGGAACTGGGCTAAACAATCTTTATTATCATTATACTTTGAGATAATTCATGGTGTCTTGAAAAACGTTGATAGAGAGGTTGTTAGTGAAGCTATCAATATCATGAACAGATCTAACGATGCTTTGATTAAATTCATGGAATACCATATCTCTAACACTGATGAAACAAAAGGTGAAAACTATCAATTGGTTAAAACTCTTGGTGAGCAGTTGATTGAAAACTGTAAACAAGTTTTGGATGTTGATCCAGTTTACAAAGATGTTGCTAAGCCTACCGGTCCAAAAACTGCTATTGACAAGAACGGTAACATTACATACTCAGAAGAGCCAAGAGAAAAGGTTAGGAAATTATCTCAATACGTACAAGAAATGGCCCTTGGTGGTCCAATCACCAAAGAATCTCAACCTACTATTGAAGAGGATTTGACTCGTGTTTACAAGGCAATCAGTGCTCAAGCTGATAAACAAGATATTTCCAGCTCCACCAGGGTTGAATTTGAAAAACTATATAGTGATTTGATGAAGTTCTTGGAAAGCTCCAAAGAAATCGATCCTTCTCAAACAACCCAATTGGCCGGTATGGATGTTGAGGATGCTTTGGACAAAGATTCCACCAAAGAAGTTGCTTCTTTGCCAAACAAATCTACCATTTCTAAGACGGTATCTTCAACTATTCCAAGAGAAACTATTCCGTTCTTACATTTGAGAAAGAAGACTCCTGCCGGAGATTGGAAATATGACCGCCAATTGTCTTCTCTTTTCTTAGATGGTTTAGAAAAGGCTGCCTTCAACGGTGTCACCTTCAAGGACAAATACGTCTTGATCACTGGTGCTGGTAAGGGTTCTATTGGTGCTGAAGTCTTGCAAGGTTTGTTACAAGGTGGTGCTAAGGTTGTTGTTACCACCTCTCGTTTCTCTAAGCAAGTTACAGACTACTACCAATCCATTTACGCCAAATATGGTGCTAAGGGTTCTACTTTGATTGTTGTTCCATTCAACCAAGGTTCTAAGCAAGACGTTGAAGCTTTGATTGAATTTATCTACGACACTGAAAAGAATGGTGGTTTAGGTTGGGATCTAGATGCTATTATTCCATTCGCGGCCATTCCAGAACAAGGTATTGAATTAGAACATATTGATTCTAAGTCTGAATTTGCTCATAGAATCATGTTGACCAATATCTTAAGAATGATGGGTTGTGTCAAGAAGCAAAAATCTGCAAGAGGTATTGAAACAAGACCAGCTCAAGTCATTCTACCAATGTCTCCAAACCATGGTACTTTCGGTGGTGATGGTtgagacc >FAS2_CDS_Part3 (SEQ ID NO: 36)ggtctcaTGGTATGTATTCAGAATCCAAGTTGTCTTTGGAAACTTTGTTCAACAGATGGCACTCTGAATCCTGGGCCAATCAATTAACCGTTTGCGGTGCTATTATTGGTTGGACTAGAGGTACTGGTTTAATGAGCGCTAATAACATCATTGCTGAAGGCATTGAAAAGATGGGTGTTCGTACTTTCTCTCAAAAGGAAATGGCTTTCAACTTATTGGGTCTATTGACTCCAGAAGTCGTAGAATTGTGCCAAAAATCACCTGTTATGGCTGACTTGAATGGTGGTTTGCAATTTGTTCCTGAATTGAAGGAATTCACTGCTAAATTGCGTAAAGAGTTGGTTGAAACTTCTGAAGTTAGAAAGGCAGTTTCCATCGAAACTGCTTTGGAGCATAAGGTTGTCAATGGCAATAGCGCTGATGCTGCATATGCTCAAGTCGAAATTCAACCAAGAGCTAACATTCAACTGGACTTCCCAGAATTGAAACCATACAAACAGGTTAAACAAATTGCTCCCGCTGAGCTTGAAGGTTTGTTGGATTTGGAAAGAGTTATTGTAGTTACCGGTTTTGCTGAAGTCGGCCCATGGGGTTCGGCCAGAACAAGATGGGAAATGGAAGCTTTTGGTGAATTTTCGTTGGAAGGTTGCGTTGAAATGGCCTGGATTATGGGCTTCATTTCATACCATAACGGTAATTTGAAGGGTCGTCCATACACTGGTTGGGTTGATTCCAAAACAAAAGAACCAGTTGATGACAAGGACGTTAAGGCCAAGTATGAAACATCAATCCTAGAACACAGTGGTATCAGATTGATCGAACCAGAGTTATTCAATGGTTACAACCCAGAAAAGAAGGAAATGATTCAAGAAGTCATTGTCGAAGAAGACTTGGAACCATTTGAGGCTTCGAAGGAAACTGCCGAACAATTTAAACACCAACATGGTGACAAAGTGGATATCTTCGAAATCCCAGAAACAGGAGAGTACTCTGTTAAGTTACTAAAGGGTGCCACTTTATACATTCCAAAGGCTTTGAGATTTGACCGTTTGGTTGCAGGTCAAATTCCAACTGGTTGGAATGCTAAGACTTATGGTATCTCTGATGATATCATTTCTCAGGTTGACCCAATCACATTATTCGTTCTCGTCTCTGTTGtgagacc >FAS2_CDS_Part4 (SEQ ID NO: 37)GGTCTCTGTTGTGGAAGCATTTATTGCATCTGGTATCACCGACCCATACGAAATGTACAAATACGTACATGTTTCTGAGGTTGGTAACTGTTCTGGTTCTGGTATGGGTGGTGTTTCTGCCTTACGTGGTATGTTTAAGGACCGTTTCAAGGATGAGCCTGTCCAAAATGATATTTTACAAGAATCATTTATCAACACCATGTCCGCTTGGGTTAATATGTTGTTGATTTCCTCATCTGGTCCAATCAAGACACCTGTTGGTGCCTGTGCCACATCCGTGGAATCTGTTGACATTGGTGTAGAAACCATCTTGTCTGGTAAGGCTAGAATCTGTATTGTCGGTGGTTACGATGATTTCCAAGAAGAAGGCTCCTTTGAGTTCGGTAACATGAAGGCCACTTCCAACACTTTGGAAGAATTTGAACATGGTCGTACCCCAGCGGAAATGTCCAGACCTGCCACCACTACCCGTAACGGTTTTATGGAAGCTCAAGGTGCTGGTATTCAAATCATCATGCAAGCTGATTTAGCTTTGAAGATGGGTGTGCCAATTTACGGTATTGTTGCCATGGCTGCTACCGCCACCGATAAGATTGGTAGATCTGTGCCAGCTCCAGGTAAGGGTATTTTAACCACTGCTCGTGAACACCACTCCAGTGTTAAGTATGCTTCACCAAACTTGAACATGAAGTACAGAAAGCGCCAATTGGTTACTCGTGAAGCTCAGATTAAAGATTGGGTAGAAAACGAATTGGAAGCTTTGAAGTTGGAGGCCGAAGAAATTCCAAGCGAAGACCAAAACGAGTTCTTACTTGAACGTACCAGAGAAATCCACAACGAAGCTGAAAGTCAATTGAGAGCTGCACAACAACAATGGGGTAACGACTTCTACAAGAGGGACCCACGTATTGCTCCATTGAGAGGAGCACTGGCTACTTACGGTTTAACTATTGATGACTTGGGTGTCGCTTCATTCCACGGtgagacc >FAS2_CDS_Part5 (SEQ ID NO: 38)ggtctcaACGGTACATCCACAAAGGCTAATGACAAGAACGAATCTGCCACAATTAATGAAATGATGAAGCATTTGGGTAGATCTGAAGGTAATCCCGTCATTGGTGTTTTCCAAAAGTTCTTGACTGGTCATCCAAAGGGTGCTGCTGGTGCATGGATGATGAATGGTGCTTTGCAAATTCTAAACAGTGGTATTATTCCAGGTAACCGTAACGCTGATAACGTGGATAAGATCTTGGAGCAATTTGAATACGTCTTGTACCCATCCAAGACTTTAAAGACCGACGGTGTCAGAGCCGTGTCCATCACTTCTTTCGGTTTTGGTCAAAAGGGTGGTCAAGCTATTGTGGTTCATCCAGACTACTTATACGGTGCTATCACTGAAGACAGATACAACGAGTATGTCGCCAAGGTTAGTGCCAGAGAGAAAAGTGCCTACAAATTCTTCCATAATGGTATGATCTACAACAAGTTGTTCGTAAGTAAAGAGCATGCTCCATACACTGATGAATTGGAAGAGGATGTTTACTTGGACCCATTAGCCCGTGTATCTAAGGATAAGAAATCAGGCTCCTTGACTTTCAACTCTAAAAACATCCAAAGCAAGGACAGTTACATCAATGCTAACACCATTGAAACTGCCAAGATGATTGAAAACATGACCAAGGAGAAAGTCTCTAACGGTGGCGTCGGTGTAGATGTTGAATTAATCACTAGCATCAACGTTGAAAATGATACTTTTATCGAGCGCAATTTCACCCCGCAAGAAATAGAGTACTGCAGCGCGCAGCCTAGTGTGCAAAGCTCTTTCGCTGGGACATGGTCCGCCAAAGAGGCTGTTTTCAAGTCCTTAGGCGTCAAGTCCTTAGGCGGTGGTGCTGCATTGAAAGACATCGAAATCGTACGCGTTAACAAAAACGCTCCAGCCGTTGAACTGCACGGTAACGCCAAAAAGGCTGCCGAAGAAGCTGGTGTTACCGATGTGAAGGTATCTATTTCTCACGATGACCTCCAAGCTGTCGCGGTCGCCGTTTCTACTAAGAAAtgagcgagacct atgccgt

For C-terminal tagging we used pAV115 as acceptor vector (Table 2) andthe following parts (BceAI site is marked in green):

>HPT1p (SEQ ID NO: 39) ggtctcacagtTCGTTTATCCTTTTTGAACTGCATCTGGCATCGTTAACAGTAAGGCCATCTGGAACATCAAGCAAGCACTCCACTTTTACGTCACAACCATAGTTGGTTAACTAAGAAAAGACAGTACATATTTCCCTTCCGAGTCACTTATTTTTTTTTTCTTCTGAAAAAATTAATTAGATTAATTTCAATTAATATCATTTCCGCTTATCTGACTTCTTTCATTTTTTTTCTCTATATTTCGCGTTTACTAGGAAAGAAAAGGAAAAAAAATTTTTCCCCCTCCATCTGTCCCAAATCGGGTAGCGATGAGCTGCTATAGAATTTTCTATTTAAACATGTTTGATAAGCCCAATTTCCGTTAGATTTTGTTCCCCCTTCGCAGTTTGGTTTGCCGTAACTTTTTTATTTTAGTCTCCATCTAGCTGGAGTAATACGATGTAGTGCCTTGTAATCTTTCTTATTTTTATATTACCGTTCGTGTTCATTATATCCATTACGTTCCCATAaatgcgagacc >HPT1t (SEQ ID NO: 40)ggtctcatgagTAGACATATCATATCCTTCAGTAACTTGAATCATACAGCAGAATTTGTACAATAGACAACGCATATAACTGCGACCATATGTATACGTATAACTAATTATTATCTCAAAGTTTATTCCCTTAGCCTCACCGGTAACCTGTGAGGCGCGATTACGTTTTCCCTCTGTTCACCACCACGTAACGCGATATTTGACACATACGttttcgagacc >HPT1_CDS (SEQ ID NO: 41)ggtctcaaATGTCGGCAAACGATAAGCAATACATCTCGTACAACAACGTACATCAACTATGTCAAGTATCCGCTGAGAGAATTAAGAATTTCAAGCCGGACTTAATCATTGCCATTGGTGGTGGTGGTTTCATTCCTGCTAGGATCCTACGTACGTTCCTAAAGGAGCCCGGCGTGCCAACCATCAGAATTTTTGCTATTATTTTGTCTTTGTACGAAGATTTGAACAGTGTAGGCTCAGAAGTTGAGGAAGTTGGTGTTAAGGTTAGCAGAACACAATGGATTGATTACGAGCAATGTAAATTAGATCTAGTCGGCAAGAACGTTCTTATCGTTGACGAAGTCGATGACACCCGTACCACACTTCATTACGCTTTGAGTGAATTGGAAAAGGATGCAGCTGAACAGGCAAAGGCTAAAGGTATCGATACTGAAAAGTCTCCAGAGATGAAAACAAACTTCGGGATTTTTGTTCTACACGATAAGCAAAAACCAAAGAAAGCAGATTTGCCTGCCGAAATGTTGAATGACAAGAACCGTTATTTTGCAGCTAAAACTGTTCCAGACAAGTGGTATGCATATCCATGGGAATCTACTGACATTGTTTTCCATACTAGAATGGCTATTGAACAGGGCAATGACATCTTTATTCCTGAGCAGGAACACAAGCAAtgagcgagacctatgccgt >GFP_tag (SEQ ID NO: 42)ggtctcaggatcaATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGAGGGGCGAAGGCGAGGGCGATGCCACCAACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTGACCTACGGCGTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCACCTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAAGGTCTATATCACCGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACGTGGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGTGCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAAtgagcgagacc >mCherry_tag (SEQ ID NO: 43)ggtctcaggatcaATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAA GTAAtgagcgagacc

For the V5 tag two oligos were ordered and annealed:

V5 oligo 1: (SEQ ID NO: 44) 5′tgtGGTAAGCCTATCCCTAACCCTCTCCTCGGACTCGATTCTACG V5 oligo 2:(SEQ ID NO: 45) 5′ taggCGTAGAATCGAGTCCGAGGAGAGGGTTAGGGATAGGCTTAC Ca

The foregoing Examples are intended to illustrate but not limit variousaspects of the disclosure.

What is claimed is:
 1. A method for making recombinant vectors suitablefor homologous recombination with each other in yeast comprising: i)providing a first recombinant vector (CDS vector) comprising a proteincoding sequence (CDS sequence) wherein the CDS is flanked on its 5′ and3′ ends by first Type IIS restriction enzyme recognition sites, the CDSvector further comprising a first antibiotic resistance gene; ii)providing a second recombinant vector (PRO vector) comprising a promotersequence (PRO sequence) wherein the PRO sequence is flanked on its 5′and 3′ ends by the first Type IIS restriction enzyme recognition sites,the PRO vector further comprising the first antibiotic resistance gene;iii) providing a third recombinant vector (TER vector) comprising atranscription termination sequence (TER sequence) wherein the TERsequence is flanked on its 5′ and 3′ ends by the first restriction TypeIIS enzyme recognition sites, the TER vector further comprising thefirst antibiotic resistance gene; iv) providing a fourth recombinantvector (LVA vector) comprising a first left adapter polynucleotidesequence (LVA sequence) wherein the LVA sequence is flanked on its 5′and 3′ ends by the first Type IIS restriction enzyme recognition sites,the LVA vector further comprising the first antibiotic resistance gene;v) providing a fifth recombinant vector (RVA vector) comprising a firstright adapter polynucleotide sequence (RVA sequence) wherein the RVAsequence is flanked on its 5′ and 3′ ends by the first Type IISrestriction enzyme recognition sites, the RVA vector further comprisingthe first antibiotic resistance gene; vi) providing a sixth recombinantvector (acceptor vector) comprising a segment, the segment comprising apolynucleotide sequence encoding a detectable marker (detectable markersequence), wherein the detectable marker sequence is flanked by thefirst Type IIS restriction enzyme recognition sites, and wherein thesegment is flanked by a second Type IIS restriction enzyme recognitionsites, wherein the acceptor vector comprises a second antibioticresistance gene but does not comprise the first antibiotic resistancegene; vii) incubating the CDS vector, the PRO vector, the TER vector,the LVA vector, the RVA vector, and the acceptor vector in a singlereaction container with a first Type IIS restriction endonuclease thatrecognizes the first Type IIS restriction endonuclease recognition siteand a DNA ligase enzyme such that ligated vectors are produced, whereinthe ligated vectors comprise sequentially the LVA sequence, the PROsequence, the CDS sequence, the TER sequence, and the RVA sequence(LVA-TU-RVA vectors), wherein the PRO, CDS and TER sequences comprise atranscription unit (TU), and wherein the LVA-TU-RVA vectors comprise thesecond antibiotic resistance gene, but do not comprise the firstantibiotic resistance gene, wherein the LVA-TU-RVA vectors do notcomprise the detectable marker sequence, and wherein the ligated vectorsdo not comprise the first Type IIS restriction site, but do comprise thesecond Type IIS restriction site; viii) introducing the LVA-TU-RVAvectors from vii) into bacteria and culturing the bacteria with aculture medium comprising an antibiotic to which bacteria comprising theLVA-TU-RVA vectors are resistant via expression of the second antibioticresistance gene such that clonal colonies of the bacteria comprising theVEGAS vectors are formed, wherein the clonal colonies do not express thedetectable marker; and viii) isolating the LVA-TU-RVA vectors from thecolonies that do not express the detectable marker to obtain isolatedLVA-TU-RVA vectors.
 2. The method of claim 1, wherein in steps i)-vi):a) the CDS sequence comprises on its 5′ end the sequence: AATG and atits 3′ end the sequence TGAG; and b) the PRO sequence comprises at its5′ end the sequence: CAGT and at its 3′ end the sequence AATG; and c)the TER sequence comprises at its 5′ end the sequence TGAG and at its 3′end the sequence TTTT; and d) the LVA sequence comprises at its 5′ endthe sequence CCTG and at its 3′ end the sequence CAGT; and; e) the RVAsequence comprises at its 5′ end TTTT and at its 3′ end the sequenceAACT; and f) the detectable marker sequence comprises at its 5′ end thesequence CCTG and at its 3′ end the sequence AACT.
 3. The method ofclaim 1, wherein the LVA sequence and the RVA sequence on eachLVA-TU-RVA vector each comprise between 35-500 base pairs, inclusive,and comprise between 30% and 70% GC base pair composition, and are lessthan 90% identical in nucleotide sequence to each other, and are lessthan 90% identical to any contiguous base pair sequence in the genome ofa yeast into which the RVA and LVA sequences are intended to beintroduced, and wherein the contiguous base pair sequence is the samelength as the LVA and the RVA.
 4. The method of claim 1, wherein thefirst LVA sequence comprises or consists of the sequence: (VA1*)(SEQ ID NO: 1) CCCCTTAGGTTGCAAATGCTCCGTCGACGGGATCTGTCCTTCTCTGCCGGCGATCGT.


5. The method of claim 1, wherein the first RVA sequence comprises orconsists of the sequence: (VA2**) (SEQ ID NO: 1)TGACGCTTGGATGCGTGACCCCGTACGTCATGACCCGTCATGGGTATG TAAGCGAAG.


6. A method for producing a homologously recombined DNA moleculecomprising distinct transcription units (TU) of claim 1, the methodcomprising: i) providing a plurality of LVA-TU-RVA vectors obtainedusing the method of claim 1, wherein each LVA-TU-RVA vector in theplurality comprises a distinct TU that comprises a distinct codingsequence (CDS), and wherein each LVA-TU-RVA vector further comprises aleft adapter polynucleotide sequence (LVA sequence) and a right adapterpolynucleotide sequence (RVA sequence), wherein only one LVA-TU-RVAvector in the plurality comprises a first LVA sequence (VA1 sequence)that is identical to a first LVA sequence in a yeast VEGAS acceptorvector, and wherein only one LVA-TU-RVA vector in the pluralitycomprises a first RVA sequence (VA2 sequence) that is identical to afirst RVA sequence in the yeast VEGAS acceptor vector; ii) linearizingthe plurality of LVA-TU-RVA vectors by digestion with a Type IISrestriction enzyme that recognizes the second Type IIS restriction siteof claim 1 to obtain distinct linearized LVA-TU-RVA vector fragmentsthat comprise the distinct TUs; iii) providing a linearized yeast VEGASacceptor vector that comprises at one end the VA1 sequence and at theother end the VA2 sequence, the linearized yeast VEGAS acceptor vectorfurther comprising a sequence encoding selectable marker functional inbacteria, a selectable marker functional in yeast, a yeast centromere(CEN) sequence, and a yeast autonomously replicating sequences (ARS);iv) introducing into the yeast the linearized yeast VEGAS acceptorvector and the distinct linearized LVA-TU-RVA vector fragments thatcomprise the distinct TUs; v) allowing homologous recombination in theyeast so that the only one LVA-TU-RVA vector segment comprising the VA1sequence and the only one LVA-TU-RVA vector segment comprising the VA2sequence are homologously recombined with the linearized yeast VEGASacceptor vector to form circularized double stranded DNA polynucleotidescomprising at least the two distinct TUs, and optionally, vi) isolatingthe circularized double stranded DNA polynucleotides from the yeast. 7.The method of claim 6, wherein in i) the plurality of LVA-TU-RVA vectorscomprises at least one, two, three or four additional distinctLVA-TU-RVA vectors.
 8. The method of claim 6, wherein the LVA sequenceand the RVA sequence on each LVA-TU-RVA vector each comprise between35-500 base pairs, comprise between 30% and 70% GC base paircomposition, are less than 90% identical in nucleotide sequence to eachother, and are less than 90% identical to any contiguous base pairsequence in the genome of the yeast wherein the contiguous sequence isthe same length as the LVA and the RVA.
 9. The method of claim 6,wherein the VA1 sequence comprises or consists of the sequence: (VA1*)(SEQ ID NO: 1) CCCCTTAGGTTGCAAATGCTCCGTCGACGGGATCTGTCCTTCTCTGCCGGCGATCGT.


10. The method of claim 6, wherein the VA2 sequence comprises orconsists of the sequence: (VA2**) (SEQ ID NO: 2)TGACGCTTGGATGCGTGACCCCGTACGTCATGACCCGTCATGGGTATG TAAGCGAAG.


11. The method of claim 6, wherein the VA1 sequence comprises orconsists of the sequence:CCCCTTAGGTTGCAAATGCTCCGTCGACGGGATCTGTCCTTCTCTGCCGGCGATCGT (VA1*) (SEQ IDNO:1) and wherein the VA2 sequence comprises or consists of thesequence: (VA2**) (SEQ ID NO: 2)TGACGCTTGGATGCGTGACCCCGTACGTCATGACCCGTCATGGGTATG TAAGCGAAG.


12. The method of claim 11, wherein the plurality of LVA-TU-RVA vectorscomprises one, two, three or four additional distinct LVA-TU-RVAvectors, wherein each of the additional LVA-TU-RVA vectors comprises anLVA sequence and an RVA sequence selected from the group consisting of:VA1* CCCCTTAGGTTGCAAATGCTCCGTCGACGGGATCTGTCCTTCTCTGCCGGCGATCGT (SEQ IDNO:1); VA2** TGACGCTTGGATGCGTGACCCCGTACGTCATGACCCGTCATGGGTATGTAAGCGAAG(SEQ ID NO:2); VA3GGAGGTACTGGCCTAGCGTCGTGGCCCGGGAGAGACAGTTTAGTAGTGACTCGCGG C (SEQ IDNO:16); VA4 TTGGCGTTAATTGTAGCTTATTTCCCGCCCTGTGATTGAGGCGGGATGGTGTCCCCA(SEQ ID NO:17); VA5GACTAAGACTCTGGTCACGGTTCAGAAGTGGACGATGCATGTCGTCGGGCTGATAG A (SEQ IDNO:18); VA6 TGCACGGCGCTAGGTGTGATATCGTACACTTGGGAGAAGTCAGATACGATTGCGGCT(SEQ ID NO:19); VA7TAGCGGCGCCGGGAAATCCAGCATATTCTCGCGGCCCTGAGCAGTAGGTGTCTCGG G (SEQ IDNO:20); VA8 GAGTCTACGTTACACCTGAACTCGCATGTCTGGGGTTGTGGTCAGGCCTTGTCAATT(SEQ ID NO:21); VA9GCGTACTGGCCGCCCGGGCCTGATGTGGCCGTCCTATTAGCATTGTACACCCTCATT (SEQ IDNO:22); VA10 CTTGAATCGGCTTTAGGATCCGGTACTGCCGACGCACTTTAGAACGGCCACCGTCCT(SEQ ID NO:23); VA11GCAAGTTTTGAAGAGGTGTAAACTCTCCGCAGCACCTCCGGACTATGCCCGAGTGGT (SEQ IDNO:24); VA12 TGAAGCTACGCGCCGAGCGTCTGACTCCTTTAGTCCGCGTCATCGCTTTGAGCGCGT(SEQ ID NO:25); VA13TCCGGATCCCTTTCGGTCCATATAGCGGATTTCCATAGACGTAGACCGCGCCAATGT (SEQ IDNO:26); VA14 GACGACGCGTTCTGTGTCTTCGTTGCGGCTCTGCGCTTGGTCGTTGGCGACGGCCGT(SEQ ID NO:27); VA15TGTAAGGGCGTCTGTTAACCCAAGGTCCCTCGAACCGTATGCAGAGCCGTGGCTACG (SEQ IDNO:28); VA16 TATCGCGGGTGCGTGCATCGACAAGCCATGCCCACCTTCTGGTCGATTGGGCTGGCG(SEQ ID NO:29); VA17CATCCATCGATATTTGGCACTGGACCTCAACGCTAGTGTTCGCGGACTGCACTACCT (SEQ IDNO:30); VA 18; GATTAAGGGGCATACCGTGCCTATCCTGGTAATTGTGTAGGCTACCTGTCTGTATAC(SEQ ID NO:31); and combinations thereof.
 13. Yeast cells comprising ahomologously recombined DNA molecule made by the process of claim
 6. 14.The yeast cells of claim 13, wherein the homologously recombined DNAmolecule comprises at least one, two, three or four additional distincttranscription units (TUs), wherein each TU encodes a distinctpolypeptide that is not endogenous to the yeast cells.
 15. The yeastcells of claim 14, wherein the distinct polypeptides are components of abiosynthetic pathway.
 16. Homologously recombined DNA molecules isolatedfrom the yeast cells of claim
 13. 17. The homologously recombined DNAmolecules of claim 16 comprising more than two distinct TUs.
 18. Thehomologously recombined DNA molecules of claim 16 comprising at leastsix distinct TUs.